1
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Vermeulen BJ, Böhler A, Gao Q, Neuner A, Župa E, Chu Z, Würtz M, Jäkle U, Gruss OJ, Pfeffer S, Schiebel E. γ-TuRC asymmetry induces local protofilament mismatch at the RanGTP-stimulated microtubule minus end. EMBO J 2024:10.1038/s44318-024-00087-4. [PMID: 38600243 DOI: 10.1038/s44318-024-00087-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
The γ-tubulin ring complex (γ-TuRC) is a structural template for de novo microtubule assembly from α/β-tubulin units. The isolated vertebrate γ-TuRC assumes an asymmetric, open structure deviating from microtubule geometry, suggesting that γ-TuRC closure may underlie regulation of microtubule nucleation. Here, we isolate native γ-TuRC-capped microtubules from Xenopus laevis egg extract nucleated through the RanGTP-induced pathway for spindle assembly and determine their cryo-EM structure. Intriguingly, the microtubule minus end-bound γ-TuRC is only partially closed and consequently, the emanating microtubule is locally misaligned with the γ-TuRC and asymmetric. In the partially closed conformation of the γ-TuRC, the actin-containing lumenal bridge is locally destabilised, suggesting lumenal bridge modulation in microtubule nucleation. The microtubule-binding protein CAMSAP2 specifically binds the minus end of γ-TuRC-capped microtubules, indicating that the asymmetric minus end structure may underlie recruitment of microtubule-modulating factors for γ-TuRC release. Collectively, we reveal a surprisingly asymmetric microtubule minus end protofilament organisation diverging from the regular microtubule structure, with direct implications for the kinetics and regulation of nucleation and subsequent modulation of microtubules during spindle assembly.
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Affiliation(s)
- Bram Ja Vermeulen
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Anna Böhler
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Qi Gao
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Erik Župa
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Zhenzhen Chu
- Institut für Genetik, Universität Bonn, Bonn, Germany
- Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education, Beijing), Lymphoma Department, Peking University Cancer Hospital & Institute, Beijing, China
| | - Martin Würtz
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | - Ursula Jäkle
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany
| | | | - Stefan Pfeffer
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany.
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie, Universität Heidelberg, DKFZ-ZMBH Allianz, Heidelberg, Germany.
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2
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Haas S, Sun X, Conceição ALC, Horbach J, Pfeffer S. The new small-angle X-ray scattering beamline for materials research at PETRA III: SAXSMAT beamline P62. J Synchrotron Radiat 2023; 30:1156-1167. [PMID: 37860939 PMCID: PMC10624033 DOI: 10.1107/s1600577523008603] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Accepted: 09/28/2023] [Indexed: 10/21/2023]
Abstract
The SAXSMAT beamline P62 (Small-Angle X-ray Scattering beamline for Materials Research) is a new beamline at the high-energy storage ring PETRA III at DESY. This beamline is dedicated to combined small- and wide-angle X-ray scattering (SAXS/WAXS) techniques for both soft and hard condensed matter systems. It works mainly in transmission geometry. The beamline covers an energy range from 3.5 keV to 35.0 keV, which fulfills the requirements of the user community to perform anomalous scattering experiments. Mirrors are used to reduce the intensity of higher harmonics. Furthermore, the mirrors and 2D compound refracting lenses can focus the beam down to a few micrometres at the sample position. This option with the high photon flux enables also SAXS/WAXS tensor tomography experiments to be performed at this new beamline in a relatively short time. The first SAXS/WAXS pattern was collected in August 2021, while the first user experiment was carried out two months later. Since January 2022 the beamline has been in regular user operation mode. In this paper the beamline optics and the SAXS/WAXS instrument are described and two examples are briefly shown.
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Affiliation(s)
- S. Haas
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
| | - X. Sun
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
| | - A. L. C. Conceição
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
| | - J. Horbach
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
| | - S. Pfeffer
- Deutsches Elektronen-Synchrotron (DESY), Notkestrasse 85, Hamburg 22607, Germany
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3
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Groh C, Haberkant P, Stein F, Filbeck S, Pfeffer S, Savitski MM, Boos F, Herrmann JM. Mitochondrial dysfunction rapidly modulates the abundance and thermal stability of cellular proteins. Life Sci Alliance 2023; 6:e202201805. [PMID: 36941057 PMCID: PMC10027898 DOI: 10.26508/lsa.202201805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 03/03/2023] [Accepted: 03/03/2023] [Indexed: 03/23/2023] Open
Abstract
Cellular functionality relies on a well-balanced, but highly dynamic proteome. Dysfunction of mitochondrial protein import leads to the cytosolic accumulation of mitochondrial precursor proteins which compromise cellular proteostasis and trigger a mitoprotein-induced stress response. To dissect the effects of mitochondrial dysfunction on the cellular proteome as a whole, we developed pre-post thermal proteome profiling. This multiplexed time-resolved proteome-wide thermal stability profiling approach with isobaric peptide tags in combination with a pulsed SILAC labelling elucidated dynamic proteostasis changes in several dimensions: In addition to adaptations in protein abundance, we observed rapid modulations of the thermal stability of individual cellular proteins. Different functional groups of proteins showed characteristic response patterns and reacted with group-specific kinetics, allowing the identification of functional modules that are relevant for mitoprotein-induced stress. Thus, our new pre-post thermal proteome profiling approach uncovered a complex response network that orchestrates proteome homeostasis in eukaryotic cells by time-controlled adaptations of the abundance and the conformation of proteins.
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Affiliation(s)
- Carina Groh
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany
| | - Per Haberkant
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | - Frank Stein
- Proteomics Core Facility, EMBL Heidelberg, Heidelberg, Germany
| | | | | | | | - Felix Boos
- Cell Biology, University of Kaiserslautern, Kaiserslautern, Germany;
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4
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Filbeck S, Cerullo F, Pfeffer S, Joazeiro CAP. Ribosome-associated quality-control mechanisms from bacteria to humans. Mol Cell 2022; 82:1451-1466. [PMID: 35452614 PMCID: PMC9034055 DOI: 10.1016/j.molcel.2022.03.038] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 03/23/2022] [Accepted: 03/28/2022] [Indexed: 11/16/2022]
Abstract
Ribosome-associated quality-control (RQC) surveys incomplete nascent polypeptides produced by interrupted translation. Central players in RQC are the human ribosome- and tRNA-binding protein, NEMF, and its orthologs, yeast Rqc2 and bacterial RqcH, which sense large ribosomal subunits obstructed with nascent chains and then promote nascent-chain proteolysis. In canonical eukaryotic RQC, NEMF stabilizes the LTN1/Listerin E3 ligase binding to obstructed ribosomal subunits for nascent-chain ubiquitylation. Furthermore, NEMF orthologs across evolution modify nascent chains by mediating C-terminal, untemplated polypeptide elongation. In eukaryotes, this process exposes ribosome-buried nascent-chain lysines, the ubiquitin acceptor sites, to LTN1. Remarkably, in both bacteria and eukaryotes, C-terminal tails also have an extra-ribosomal function as degrons. Here, we discuss recent findings on RQC mechanisms and briefly review how ribosomal stalling is sensed upstream of RQC, including via ribosome collisions, from an evolutionary perspective. Because RQC defects impair cellular fitness and cause neurodegeneration, this knowledge provides a framework for pathway-related biology and disease studies.
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Affiliation(s)
- Sebastian Filbeck
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Federico Cerullo
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany.
| | - Claudio A P Joazeiro
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Florida, Jupiter, FL 33458, USA.
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5
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Cerullo F, Filbeck S, Patil PR, Hung HC, Xu H, Vornberger J, Hofer FW, Schmitt J, Kramer G, Bukau B, Hofmann K, Pfeffer S, Joazeiro CAP. Bacterial ribosome collision sensing by a MutS DNA repair ATPase paralogue. Nature 2022; 603:509-514. [PMID: 35264791 DOI: 10.1038/s41586-022-04487-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/28/2022] [Indexed: 12/12/2022]
Abstract
Ribosome stalling during translation is detrimental to cellular fitness, but how this is sensed and elicits recycling of ribosomal subunits and quality control of associated mRNA and incomplete nascent chains is poorly understood1,2. Here we uncover Bacillus subtilis MutS2, a member of the conserved MutS family of ATPases that function in DNA mismatch repair3, as an unexpected ribosome-binding protein with an essential function in translational quality control. Cryo-electron microscopy analysis of affinity-purified native complexes shows that MutS2 functions in sensing collisions between stalled and translating ribosomes and suggests how ribosome collisions can serve as platforms to deploy downstream processes: MutS2 has an RNA endonuclease small MutS-related (SMR) domain, as well as an ATPase/clamp domain that is properly positioned to promote ribosomal subunit dissociation, which is a requirement both for ribosome recycling and for initiation of ribosome-associated protein quality control (RQC). Accordingly, MutS2 promotes nascent chain modification with alanine-tail degrons-an early step in RQC-in an ATPase domain-dependent manner. The relevance of these observations is underscored by evidence of strong co-occurrence of MutS2 and RQC genes across bacterial phyla. Overall, the findings demonstrate a deeply conserved role for ribosome collisions in mounting a complex response to the interruption of translation within open reading frames.
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Affiliation(s)
- Federico Cerullo
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Sebastian Filbeck
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Pratik Rajendra Patil
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Hao-Chih Hung
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Haifei Xu
- Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA
| | - Julia Vornberger
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Florian W Hofer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Jaro Schmitt
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Guenter Kramer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Bernd Bukau
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Kay Hofmann
- Institute for Genetics, University of Cologne, Cologne, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany.
| | - Claudio A P Joazeiro
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Heidelberg, Germany. .,Department of Molecular Medicine, Scripps Florida, Jupiter, FL, USA.
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6
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Würtz M, Zupa E, Atorino ES, Neuner A, Böhler A, Rahadian AS, Vermeulen BJA, Tonon G, Eustermann S, Schiebel E, Pfeffer S. Modular assembly of the principal microtubule nucleator γ-TuRC. Nat Commun 2022; 13:473. [PMID: 35078983 PMCID: PMC8789826 DOI: 10.1038/s41467-022-28079-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 01/07/2022] [Indexed: 12/15/2022] Open
Abstract
AbstractThe gamma-tubulin ring complex (γ-TuRC) is the principal microtubule nucleation template in vertebrates. Recent cryo-EM reconstructions visualized the intricate quaternary structure of the γ-TuRC, containing more than thirty subunits, raising fundamental questions about γ-TuRC assembly and the role of actin as an integral part of the complex. Here, we reveal the structural mechanism underlying modular γ-TuRC assembly and identify a functional role of actin in microtubule nucleation. During γ-TuRC assembly, a GCP6-stabilized core comprising GCP2-3-4-5-4-6 is expanded by stepwise recruitment, selective stabilization and conformational locking of four pre-formed GCP2-GCP3 units. Formation of the lumenal bridge specifies incorporation of the terminal GCP2-GCP3 unit and thereby leads to closure of the γ-TuRC ring in a left-handed spiral configuration. Actin incorporation into the complex is not relevant for γ-TuRC assembly and structural integrity, but determines γ-TuRC geometry and is required for efficient microtubule nucleation and mitotic chromosome alignment in vivo.
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7
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Waltz F, Salinas-Giegé T, Englmeier R, Meichel H, Soufari H, Kuhn L, Pfeffer S, Förster F, Engel BD, Giegé P, Drouard L, Hashem Y. How to build a ribosome from RNA fragments in Chlamydomonas mitochondria. Nat Commun 2021; 12:7176. [PMID: 34887394 PMCID: PMC8660880 DOI: 10.1038/s41467-021-27200-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 11/08/2021] [Indexed: 01/12/2023] Open
Abstract
Mitochondria are the powerhouse of eukaryotic cells. They possess their own gene expression machineries where highly divergent and specialized ribosomes, named hereafter mitoribosomes, translate the few essential messenger RNAs still encoded by mitochondrial genomes. Here, we present a biochemical and structural characterization of the mitoribosome in the model green alga Chlamydomonas reinhardtii, as well as a functional study of some of its specific components. Single particle cryo-electron microscopy resolves how the Chlamydomonas mitoribosome is assembled from 13 rRNA fragments encoded by separate non-contiguous gene pieces. Additional proteins, mainly OPR, PPR and mTERF helical repeat proteins, are found in Chlamydomonas mitoribosome, revealing the structure of an OPR protein in complex with its RNA binding partner. Targeted amiRNA silencing indicates that these ribosomal proteins are required for mitoribosome integrity. Finally, we use cryo-electron tomography to show that Chlamydomonas mitoribosomes are attached to the inner mitochondrial membrane via two contact points mediated by Chlamydomonas-specific proteins. Our study expands our understanding of mitoribosome diversity and the various strategies these specialized molecular machines adopt for membrane tethering.
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Affiliation(s)
- Florent Waltz
- Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 2 rue R. Escarpit, 33600, Pessac, France
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, 67084, Strasbourg, France
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
| | - Thalia Salinas-Giegé
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, 67084, Strasbourg, France
| | - Robert Englmeier
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Herrade Meichel
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, 67084, Strasbourg, France
| | - Heddy Soufari
- Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 2 rue R. Escarpit, 33600, Pessac, France
| | - Lauriane Kuhn
- Plateforme protéomique Strasbourg Esplanade FRC1589 du CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Friedrich Förster
- Structural Biochemistry, Bijvoet Centre for Biomolecular Research, Utrecht University, Universiteitsweg 99, 3584 CG, Utrecht, The Netherlands
| | - Benjamin D Engel
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
- Department of Chemistry, Technical University of Munich, Lichtenbergstraße 4, 85748, Garching, Germany
| | - Philippe Giegé
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, 67084, Strasbourg, France.
| | - Laurence Drouard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 12 rue du général Zimmer, 67084, Strasbourg, France.
| | - Yaser Hashem
- Institut Européen de Chimie et Biologie, U1212 Inserm, Université de Bordeaux, 2 rue R. Escarpit, 33600, Pessac, France.
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8
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Moebel E, Martinez-Sanchez A, Lamm L, Righetto RD, Wietrzynski W, Albert S, Larivière D, Fourmentin E, Pfeffer S, Ortiz J, Baumeister W, Peng T, Engel BD, Kervrann C. Author Correction: Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms. Nat Methods 2021; 19:129. [PMID: 34785810 DOI: 10.1038/s41592-021-01349-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Emmanuel Moebel
- Serpico Project-Team, Centre Inria Rennes-Bretagne Atlantique and CNRS-UMR 144, Inria, CNRS, Institut Curie, PSL Research University, Campus Universitaire de Beaulieu, Rennes Cedex, France
| | - Antonio Martinez-Sanchez
- Department of Computer Science, Faculty of Sciences, University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario s/n, Oviedo, Spain.,Institute of Neuropathology, Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells', University of Göttingen, Göttingen, Germany
| | - Lorenz Lamm
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.,Helmholtz AI, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ricardo D Righetto
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Damien Larivière
- Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France
| | - Eric Fourmentin
- Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France
| | - Stefan Pfeffer
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Julio Ortiz
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Ernst Ruska-Centre, Wilhelm-Johnen-Straße, Jülich, Germany
| | | | - Tingying Peng
- Helmholtz AI, Helmholtz Zentrum München, Neuherberg, Germany
| | - Benjamin D Engel
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany. .,Department of Chemistry, Technical University of Munich, Garching, Germany.
| | - Charles Kervrann
- Serpico Project-Team, Centre Inria Rennes-Bretagne Atlantique and CNRS-UMR 144, Inria, CNRS, Institut Curie, PSL Research University, Campus Universitaire de Beaulieu, Rennes Cedex, France.
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9
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Moebel E, Martinez-Sanchez A, Lamm L, Righetto RD, Wietrzynski W, Albert S, Larivière D, Fourmentin E, Pfeffer S, Ortiz J, Baumeister W, Peng T, Engel BD, Kervrann C. Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms. Nat Methods 2021; 18:1386-1394. [PMID: 34675434 DOI: 10.1038/s41592-021-01275-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Accepted: 08/18/2021] [Indexed: 11/10/2022]
Abstract
Cryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. However, automated identification of macromolecules inside cellular tomograms is challenged by noise and reconstruction artifacts, as well as the presence of many molecular species in the crowded volumes. Here, we present DeepFinder, a computational procedure that uses artificial neural networks to simultaneously localize multiple classes of macromolecules. Once trained, the inference stage of DeepFinder is faster than template matching and performs better than other competitive deep learning methods at identifying macromolecules of various sizes in both synthetic and experimental datasets. On cellular cryo-ET data, DeepFinder localized membrane-bound and cytosolic ribosomes (roughly 3.2 MDa), ribulose 1,5-bisphosphate carboxylase-oxygenase (roughly 560 kDa soluble complex) and photosystem II (roughly 550 kDa membrane complex) with an accuracy comparable to expert-supervised ground truth annotations. DeepFinder is therefore a promising algorithm for the semiautomated analysis of a wide range of molecular targets in cellular tomograms.
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Affiliation(s)
- Emmanuel Moebel
- Serpico Project-Team, Centre Inria Rennes-Bretagne Atlantique and CNRS-UMR 144, Inria, CNRS, Institut Curie, PSL Research University, Campus Universitaire de Beaulieu, Rennes Cedex, France
| | - Antonio Martinez-Sanchez
- Department of Computer Science, Faculty of Sciences, University of Oviedo, Oviedo, Spain.,Health Research Institute of Asturias (ISPA), Avenida Hospital Universitario s/n, Oviedo, Spain.,Institute of Neuropathology, Cluster of Excellence 'Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells', University of Göttingen, Göttingen, Germany
| | - Lorenz Lamm
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany.,Helmholtz AI, Helmholtz Zentrum München, Neuherberg, Germany
| | - Ricardo D Righetto
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany
| | | | | | - Damien Larivière
- Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France
| | - Eric Fourmentin
- Fourmentin-Guilbert Scientific Foundation, Noisy-le-Grand, France
| | - Stefan Pfeffer
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Julio Ortiz
- Max Planck Institute of Biochemistry, Martinsried, Germany.,Ernst Ruska-Centre, Wilhelm-Johnen-Straße, Jülich, Germany
| | | | - Tingying Peng
- Helmholtz AI, Helmholtz Zentrum München, Neuherberg, Germany
| | - Benjamin D Engel
- Helmholtz Pioneer Campus, Helmholtz Zentrum München, Neuherberg, Germany. .,Department of Chemistry, Technical University of Munich, Garching, Germany.
| | - Charles Kervrann
- Serpico Project-Team, Centre Inria Rennes-Bretagne Atlantique and CNRS-UMR 144, Inria, CNRS, Institut Curie, PSL Research University, Campus Universitaire de Beaulieu, Rennes Cedex, France.
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10
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Böhler A, Vermeulen BJA, Würtz M, Zupa E, Pfeffer S, Schiebel E. The gamma-tubulin ring complex: Deciphering the molecular organization and assembly mechanism of a major vertebrate microtubule nucleator. Bioessays 2021; 43:e2100114. [PMID: 34160844 DOI: 10.1002/bies.202100114] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Revised: 06/07/2021] [Accepted: 06/09/2021] [Indexed: 11/10/2022]
Abstract
Microtubules are protein cylinders with functions in cell motility, signal sensing, cell organization, intracellular transport, and chromosome segregation. One of the key properties of microtubules is their dynamic architecture, allowing them to grow and shrink in length by adding or removing copies of their basic subunit, the heterodimer αβ-tubulin. In higher eukaryotes, de novo assembly of microtubules from αβ-tubulin is initiated by a 2 MDa multi-subunit complex, the gamma-tubulin ring complex (γ-TuRC). For many years, the structure of the γ-TuRC and the function of its subunits remained enigmatic, although structural data from the much simpler yeast counterpart, the γ-tubulin small complex (γ-TuSC), were available. Two recent breakthroughs in the field, high-resolution structural analysis and recombinant reconstitution of the complex, have revolutionized our knowledge about the architecture and function of the γ-TuRC and will form the basis for addressing outstanding questions about biogenesis and regulation of this essential microtubule organizer.
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Affiliation(s)
- Anna Böhler
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Bram J A Vermeulen
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Martin Würtz
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Erik Zupa
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg, Heidelberg, Germany
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11
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Klein MC, Lerner M, Nguyen D, Pfeffer S, Dudek J, Förster F, Helms V, Lang S, Zimmermann R. TRAM1 protein may support ER protein import by modulating the phospholipid bilayer near the lateral gate of the Sec61-channel. Channels (Austin) 2021; 14:28-44. [PMID: 32013668 PMCID: PMC7039644 DOI: 10.1080/19336950.2020.1724759] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
In mammalian cells, one-third of all polypeptides is transported into or through the ER-membrane via the Sec61-channel. While the Sec61-complex facilitates the transport of all polypeptides with amino-terminal signal peptides (SP) or SP-equivalent transmembrane helices (TMH), the translocating chain-associated membrane protein (now termed TRAM1) was proposed to support transport of a subset of precursors. To identify possible determinants of TRAM1 substrate specificity, we systematically identified TRAM1-dependent precursors by analyzing cellular protein abundance changes upon TRAM1 depletion in HeLa cells using quantitative label-free proteomics. In contrast to previous analysis after TRAP depletion, SP and TMH analysis of TRAM1 clients did not reveal any distinguishing features that could explain its putative substrate specificity. To further address the TRAM1 mechanism, live-cell calcium imaging was carried out after TRAM1 depletion in HeLa cells. In additional contrast to previous analysis after TRAP depletion, TRAM1 depletion did not affect calcium leakage from the ER. Thus, TRAM1 does not appear to act as SP- or TMH-receptor on the ER-membrane’s cytosolic face and does not appear to affect the open probability of the Sec61-channel. It may rather play a supportive role in protein transport, such as making the phospholipid bilayer conducive for accepting SP and TMH in the vicinity of the lateral gate of the Sec61-channel. Abbreviations: ER, endoplasmic reticulum; OST, oligosaccharyltransferase; RAMP, ribosome-associated membrane protein; SP, signal peptide; SR, SRP-receptor; SRP, signal recognition particle; TMH, signal peptide-equivalent transmembrane helix; TRAM, translocating chain-associated membrane protein; TRAP, translocon-associated protein.
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Affiliation(s)
| | - Monika Lerner
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | | | - Johanna Dudek
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, Homburg, Germany
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12
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Würtz M, Böhler A, Neuner A, Zupa E, Rohland L, Liu P, Vermeulen BJA, Pfeffer S, Eustermann S, Schiebel E. Reconstitution of the recombinant human γ-tubulin ring complex. Open Biol 2021; 11:200325. [PMID: 33529551 PMCID: PMC8061689 DOI: 10.1098/rsob.200325] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Cryo-electron microscopy recently resolved the structure of the vertebrate γ-tubulin ring complex (γ-TuRC) purified from Xenopus laevis egg extract and human cells to near-atomic resolution. These studies clarified the arrangement and stoichiometry of γ-TuRC components and revealed that one molecule of actin and the small protein MZT1 are embedded into the complex. Based on this structural census of γ-TuRC core components, we developed a recombinant expression system for the reconstitution and purification of human γ-TuRC from insect cells. The recombinant γ-TuRC recapitulates the structure of purified native γ-TuRC and has similar functional properties in terms of microtubule nucleation and minus end capping. This recombinant system is a central step towards deciphering the activation mechanisms of the γ-TuRC and the function of individual γ-TuRC core components.
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Affiliation(s)
- Martin Würtz
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Anna Böhler
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Erik Zupa
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Lukas Rohland
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Peng Liu
- Centre for Organismal Studies Universität Heidelberg (COS), Im Neuenheimer Feld 230, D-69120 Heidelberg, Germany
| | - Bram J A Vermeulen
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
| | - Sebastian Eustermann
- European Molecular Biology Laboratory (EMBL), Heidelberg Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120 Heidelberg, Germany
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13
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Filbeck S, Cerullo F, Paternoga H, Tsaprailis G, Joazeiro CAP, Pfeffer S. Mimicry of Canonical Translation Elongation Underlies Alanine Tail Synthesis in RQC. Mol Cell 2020; 81:104-114.e6. [PMID: 33259811 DOI: 10.1016/j.molcel.2020.11.001] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Revised: 10/06/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
Aborted translation produces large ribosomal subunits obstructed with tRNA-linked nascent chains, which are substrates of ribosome-associated quality control (RQC). Bacterial RqcH, a widely conserved RQC factor, senses the obstruction and recruits tRNAAla(UGC) to modify nascent-chain C termini with a polyalanine degron. However, how RqcH and its eukaryotic homologs (Rqc2 and NEMF), despite their relatively simple architecture, synthesize such C-terminal tails in the absence of a small ribosomal subunit and mRNA has remained unknown. Here, we present cryoelectron microscopy (cryo-EM) structures of Bacillus subtilis RQC complexes representing different Ala tail synthesis steps. The structures explain how tRNAAla is selected via anticodon reading during recruitment to the A-site and uncover striking hinge-like movements in RqcH leading tRNAAla into a hybrid A/P-state associated with peptidyl-transfer. Finally, we provide structural, biochemical, and molecular genetic evidence identifying the Hsp15 homolog (encoded by rqcP) as a novel RQC component that completes the cycle by stabilizing the P-site tRNA conformation. Ala tailing thus follows mechanistic principles surprisingly similar to canonical translation elongation.
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Affiliation(s)
- Sebastian Filbeck
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Federico Cerullo
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Helge Paternoga
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | | | - Claudio A P Joazeiro
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany; Department of Molecular Medicine, Scripps Research, Jupiter, FL 33458, USA.
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Alliance, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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14
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Liu P, Würtz M, Zupa E, Pfeffer S, Schiebel E. Microtubule nucleation: The waltz between γ-tubulin ring complex and associated proteins. Curr Opin Cell Biol 2020; 68:124-131. [PMID: 33190097 DOI: 10.1016/j.ceb.2020.10.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 09/22/2020] [Accepted: 10/08/2020] [Indexed: 12/31/2022]
Abstract
Microtubules are essential cytoskeletal elements assembled from αβ-tubulin dimers. In high eukaryotes, microtubule nucleation, the de novo assembly of a microtubule from its minus end, is initiated by the γ-tubulin ring complex (γ-TuRC). Despite many years of research, the structural and mechanistic principles of the microtubule nucleation machinery remained poorly understood. Only recently, cryoelectron microscopy studies uncovered the molecular organization and potential activation mechanisms of γ-TuRC. In vitro assays further deciphered the spatial and temporal cooperation between γ-TuRC and additional factors, for example, the augmin complex, the phase separation protein TPX2, and the microtubule polymerase XMAP215. These breakthroughs deepen our understanding of microtubule nucleation mechanisms and will link the assembly of individual microtubules to the organization of cellular microtubule networks.
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Affiliation(s)
- Peng Liu
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany.
| | - Martin Würtz
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
| | - Erik Zupa
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), Im Neuenheimer Feld 282, D-69120, Heidelberg, Germany
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15
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Zupa E, Zheng A, Neuner A, Würtz M, Liu P, Böhler A, Schiebel E, Pfeffer S. The cryo-EM structure of a γ-TuSC elucidates architecture and regulation of minimal microtubule nucleation systems. Nat Commun 2020; 11:5705. [PMID: 33177498 PMCID: PMC7658347 DOI: 10.1038/s41467-020-19456-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 10/15/2020] [Indexed: 11/23/2022] Open
Abstract
The nucleation of microtubules from αβ-tubulin subunits is mediated by γ-tubulin complexes, which vary in composition across organisms. Aiming to understand how de novo microtubule formation is achieved and regulated by a minimal microtubule nucleation system, we here determined the cryo-electron microscopy structure of the heterotetrameric γ-tubulin small complex (γ-TuSC) from C. albicans at near-atomic resolution. Compared to the vertebrate γ-tubulin ring complex (γ-TuRC), we observed a vastly remodeled interface between the SPC/GCP-γ-tubulin spokes, which stabilizes the complex and defines the γ-tubulin arrangement. The relative positioning of γ-tubulin subunits indicates that a conformational rearrangement of the complex is required for microtubule nucleation activity, which follows opposing directionality as predicted for the vertebrate γ-TuRC. Collectively, our data suggest that the assembly and regulation mechanisms of γ-tubulin complexes fundamentally differ between the microtubule nucleation systems in lower and higher eukaryotes. The nucleation of microtubules from αβ-tubulin subunits is mediated by γtubulin complexes, which vary in composition across organisms. Here, authors present the cryo-EM structure of the heterotetrameric γ-tubulin small complex (γ-TuSC) from C. albicans at near-atomic resolution.
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Affiliation(s)
- Erik Zupa
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Anjun Zheng
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Annett Neuner
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Martin Würtz
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Peng Liu
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Anna Böhler
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120, Heidelberg, Germany.
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16
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Zupa E, Liu P, Würtz M, Schiebel E, Pfeffer S. The structure of the γ-TuRC: a 25-years-old molecular puzzle. Curr Opin Struct Biol 2020; 66:15-21. [PMID: 33002806 DOI: 10.1016/j.sbi.2020.08.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 08/26/2020] [Accepted: 08/28/2020] [Indexed: 10/23/2022]
Abstract
The nucleation of microtubules from αβ-tubulin dimers is an essential cellular process dependent on γ-tubulin complexes. Mechanistic understanding of the nucleation reaction was hampered by the lack of γ-tubulin complex structures at sufficiently high resolution. The recent technical developments in cryo-electron microscopy have allowed resolving the vertebrate γ-tubulin ring complex (γ-TuRC) structure at near-atomic resolution. These studies clarified the arrangement and stoichiometry of gamma-tubulin complex proteins in the γ-TuRC, characterized the surprisingly versatile integration of the small proteins MZT1/2 into the complex, and identified actin as an integral component of the γ-TuRC. In this review, we summarize the structural insights into the molecular architecture, the assembly pathway, and the regulation of the microtubule nucleation reaction.
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Affiliation(s)
- Erik Zupa
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Peng Liu
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Martin Würtz
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany
| | - Elmar Schiebel
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, DKFZ-ZMBH Allianz, Im Neuenheimer Feld 282, 69120 Heidelberg, Germany.
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17
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Wild K, Aleksić M, Lapouge K, Juaire KD, Flemming D, Pfeffer S, Sinning I. MetAP-like Ebp1 occupies the human ribosomal tunnel exit and recruits flexible rRNA expansion segments. Nat Commun 2020; 11:776. [PMID: 32034140 PMCID: PMC7005732 DOI: 10.1038/s41467-020-14603-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 01/20/2020] [Indexed: 12/13/2022] Open
Abstract
Human Ebp1 is a member of the proliferation-associated 2G4 (PA2G4) family and plays an important role in cancer regulation. Ebp1 shares the methionine aminopeptidase (MetAP) fold and binds to mature 80S ribosomes for translational control. Here, we present a cryo-EM single particle analysis reconstruction of Ebp1 bound to non-translating human 80S ribosomes at a resolution range from 3.3 to ~8 Å. Ebp1 blocks the tunnel exit with major interactions to the general uL23/uL29 docking site for nascent chain-associated factors complemented by eukaryote-specific eL19 and rRNA helix H59. H59 is defined as dynamic adaptor undergoing significant remodeling upon Ebp1 binding. Ebp1 recruits rRNA expansion segment ES27L to the tunnel exit via specific interactions with rRNA consensus sequences. The Ebp1-ribosome complex serves as a template for MetAP binding and provides insights into the structural principles for spatial coordination of co-translational events and molecular triage at the ribosomal tunnel exit. The ErbB3 receptor binding protein Ebp1 binds to ribosomes and is linked to translational control. Here, the authors present the cryo-EM structure of human Ebp1 bound to a non-translating 80S ribosome and find that Ebp1 blocks the tunnel exit and recruits the rRNA expansion segment ES27L to the tunnel exit.
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Affiliation(s)
- Klemens Wild
- Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Milan Aleksić
- Zentrum für Molekulare Biologie der Universität Heidelberg, INF282, D-69120, Heidelberg, Germany
| | - Karine Lapouge
- Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Keven D Juaire
- Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Dirk Flemming
- Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany
| | - Stefan Pfeffer
- Zentrum für Molekulare Biologie der Universität Heidelberg, INF282, D-69120, Heidelberg, Germany.
| | - Irmgard Sinning
- Biochemiezentrum der Universität Heidelberg (BZH), INF 328, D-69120, Heidelberg, Germany.
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18
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Liu P, Zupa E, Neuner A, Böhler A, Loerke J, Flemming D, Ruppert T, Rudack T, Peter C, Spahn C, Gruss OJ, Pfeffer S, Schiebel E. Insights into the assembly and activation of the microtubule nucleator γ-TuRC. Nature 2019; 578:467-471. [DOI: 10.1038/s41586-019-1896-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/10/2019] [Indexed: 02/06/2023]
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19
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Schaffer M, Pfeffer S, Mahamid J, Kleindiek S, Laugks T, Albert S, Engel BD, Rummel A, Smith AJ, Baumeister W, Plitzko JM. A cryo-FIB lift-out technique enables molecular-resolution cryo-ET within native Caenorhabditis elegans tissue. Nat Methods 2019; 16:757-762. [DOI: 10.1038/s41592-019-0497-5] [Citation(s) in RCA: 115] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Accepted: 06/18/2019] [Indexed: 01/01/2023]
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20
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Rast A, Schaffer M, Albert S, Wan W, Pfeffer S, Beck F, Plitzko JM, Nickelsen J, Engel BD. Biogenic regions of cyanobacterial thylakoids form contact sites with the plasma membrane. Nat Plants 2019; 5:436-446. [PMID: 30962530 DOI: 10.1038/s41477-019-0399-7] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 03/04/2019] [Indexed: 05/20/2023]
Abstract
Little is known about how the photosynthetic machinery is arranged in time and space during the biogenesis of thylakoid membranes. Using in situ cryo-electron tomography to image the three-dimensional architecture of the cyanobacterium Synechocystis, we observed that the tips of multiple thylakoids merge to form a substructure called the 'convergence membrane'. This high-curvature membrane comes into close contact with the plasma membrane at discrete sites. We generated subtomogram averages of 70S ribosomes and array-forming phycobilisomes, then mapped these structures onto the native membrane architecture as markers for protein synthesis and photosynthesis, respectively. This molecular localization identified two distinct biogenic regions in the thylakoid network: thylakoids facing the cytosolic interior of the cell that were associated with both marker complexes, and convergence membranes that were decorated by ribosomes but not phycobilisomes. We propose that the convergence membranes perform a specialized biogenic function, coupling the synthesis of thylakoid proteins with the integration of cofactors from the plasma membrane and the periplasmic space.
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Affiliation(s)
- Anna Rast
- Department of Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Martinsried, Germany
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Sahradha Albert
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - William Wan
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Stefan Pfeffer
- Center for Molecular Biology, University of Heidelberg, Heidelberg, Germany
| | - Florian Beck
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Jörg Nickelsen
- Department of Molecular Plant Sciences, Ludwig-Maximilians-University Munich, Martinsried, Germany.
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Martinsried, Germany.
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21
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Hausberg M, Felten H, Pfeffer S. Treatment of Chemotherapy-Induced Thrombotic Microangiopathy with Eculizumab in a Patient with Metastatic Breast Cancer. Case Rep Oncol 2019; 12:1-6. [PMID: 30792638 PMCID: PMC6381888 DOI: 10.1159/000495031] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 10/30/2018] [Indexed: 12/16/2022] Open
Abstract
The unexpected occurrence of thrombotic microangiopathy (TMA), characterised by microangiopathic haemolytic anaemia and thrombocytopenia, in a patient with cancer requires urgent diagnosis and appropriate management. TMA in patients with metastatic cancer can be a manifestation of the malignancy itself or a therapeutic complication. Distinguishing the cause of TMA is complicated but clinically important to initiate appropriate treatment of metastatic cancer and avoid potential drug toxicity. Eculizumab, which inhibits alternative complement pathway activation, has been shown to be effective in chemotherapy-induced TMA. We report the case of a 69-year-old woman with breast cancer who experienced a mitomycin-C-induced TMA manifestation. TMA did not respond to conservative therapy, plasmapheresis or rituximab and rapidly lead to dialysis dependency. Despite disease progression and metastases, eculizumab treatment was associated with recovered renal function and enabled the patient to avoid dialysis, improving her quality of life.
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Affiliation(s)
- Martin Hausberg
- Department of General Internal Medicine, Nephrology, Rheumatology and Pneumology, Karlsruhe General Hospital, Karlsruhe, Germany
| | - Helmut Felten
- Department of General Internal Medicine, Nephrology, Rheumatology and Pneumology, Karlsruhe General Hospital, Karlsruhe, Germany
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22
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Abstract
The membrane of the endoplasmic reticulum (ER) in human cells harbors the protein translocon, which facilitates membrane insertion and translocation of almost every newly synthesized polypeptide targeted to organelles of the secretory pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins, which are associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, Sec61 channel opening and closing, and modification of precursor polypeptides in transit through the Sec61 complex. Recently, cryoelectron tomography of translocons in native ER membranes has given unprecedented insights into the architecture and dynamics of the native, ribosome-associated translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion or translocation of newly synthesized polypeptides as well as the possible roles of the Sec61 channel as a passive ER calcium leak channel and regulator of ATP/ADP exchange between cytosol and ER.
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Affiliation(s)
- Sven Lang
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany.
| | - Duy Nguyen
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- ZMBH, 69120, Heidelberg, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, 82152, Martinsried, Germany
- Center for Biomolecular Research, Utrecht University, 3584 CH, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Richard Zimmermann
- Competence Center for Molecular Medicine, Saarland University Medical School, Building 44, 66421, Homburg, Germany
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23
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Pfeffer S, Mahamid J. Unravelling molecular complexity in structural cell biology. Curr Opin Struct Biol 2018; 52:111-118. [PMID: 30339965 DOI: 10.1016/j.sbi.2018.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/18/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Structural and cell biology have traditionally been separate disciplines and employed techniques that were well defined within the realm of either one or the other. Recent technological breakthroughs propelled electron microscopy of frozen hydrated specimens (cryo-EM) followed by single-particle analysis (SPA) to become a widely applied approach for obtaining near-atomic resolution structures of purified macromolecules. In parallel, ongoing developments on sample preparation are increasingly successful in bringing molecular views into cell biology. Cryo-electron tomography (cryo-ET) has so far served as the main imaging modality employed in these efforts towards obtaining three-dimensional (3D) volumes of heterogeneous molecular assemblies. We review the state-of-the-art in cryo-ET and computational processing and describe the current opportunities and frontiers for in-cell applications.
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Affiliation(s)
- Stefan Pfeffer
- Centre for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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24
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Nguyen D, Stutz R, Schorr S, Lang S, Pfeffer S, Freeze HH, Förster F, Helms V, Dudek J, Zimmermann R. Proteomics reveals signal peptide features determining the client specificity in human TRAP-dependent ER protein import. Nat Commun 2018; 9:3765. [PMID: 30217974 PMCID: PMC6138672 DOI: 10.1038/s41467-018-06188-z] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Accepted: 08/23/2018] [Indexed: 12/22/2022] Open
Abstract
In mammalian cells, one-third of all polypeptides are transported into or across the ER membrane via the Sec61 channel. While the Sec61 complex facilitates translocation of all polypeptides with amino-terminal signal peptides (SP) or transmembrane helices, the Sec61-auxiliary translocon-associated protein (TRAP) complex supports translocation of only a subset of precursors. To characterize determinants of TRAP substrate specificity, we here systematically identify TRAP-dependent precursors by analyzing cellular protein abundance changes upon TRAP depletion using quantitative label-free proteomics. The results are validated in independent experiments by western blotting, quantitative RT-PCR, and complementation analysis. The SPs of TRAP clients exhibit above-average glycine-plus-proline content and below-average hydrophobicity as distinguishing features. Thus, TRAP may act as SP receptor on the ER membrane’s cytosolic face, recognizing precursor polypeptides with SPs of high glycine-plus-proline content and/or low hydrophobicity, and triggering substrate-specific opening of the Sec61 channel through interactions with the ER-lumenal hinge of Sec61α. While Sec61 enables ER import of all polypeptides with N-terminal signal peptides, only selected clients are accepted for TRAP-assisted ER import. Here, the authors use a proteomics approach to characterize TRAP-dependent clients, identifying signal peptide features that govern recognition by TRAP.
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Affiliation(s)
- Duy Nguyen
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany
| | - Regine Stutz
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany
| | - Stefan Schorr
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany
| | - Sven Lang
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany
| | - Stefan Pfeffer
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, 82152, Martinsried, Germany
| | - Hudson H Freeze
- Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, 92037, USA
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584, CH, Utrecht, The Netherlands
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, 66041, Saarbrücken, Germany.
| | - Johanna Dudek
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany.
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421, Homburg, Germany.
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25
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Delarue M, Brittingham GP, Pfeffer S, Surovtsev IV, Pinglay S, Kennedy KJ, Schaffer M, Gutierrez JI, Sang D, Poterewicz G, Chung JK, Plitzko JM, Groves JT, Jacobs-Wagner C, Engel BD, Holt LJ. mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding. Cell 2018. [PMID: 29937223 DOI: 10.1016/j.cell.2018.1005.1042] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023]
Abstract
Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.
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Affiliation(s)
- M Delarue
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - S Pfeffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - I V Surovtsev
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA
| | - S Pinglay
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - K J Kennedy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - M Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J I Gutierrez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - D Sang
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G Poterewicz
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - J K Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA
| | - J M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - C Jacobs-Wagner
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06511, USA
| | - B D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - L J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA.
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26
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Delarue M, Brittingham GP, Pfeffer S, Surovtsev IV, Pinglay S, Kennedy KJ, Schaffer M, Gutierrez JI, Sang D, Poterewicz G, Chung JK, Plitzko JM, Groves JT, Jacobs-Wagner C, Engel BD, Holt LJ. mTORC1 Controls Phase Separation and the Biophysical Properties of the Cytoplasm by Tuning Crowding. Cell 2018; 174:338-349.e20. [PMID: 29937223 PMCID: PMC10080728 DOI: 10.1016/j.cell.2018.05.042] [Citation(s) in RCA: 229] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Revised: 03/26/2018] [Accepted: 05/17/2018] [Indexed: 12/14/2022]
Abstract
Macromolecular crowding has a profound impact on reaction rates and the physical properties of the cell interior, but the mechanisms that regulate crowding are poorly understood. We developed genetically encoded multimeric nanoparticles (GEMs) to dissect these mechanisms. GEMs are homomultimeric scaffolds fused to a fluorescent protein that self-assemble into bright, stable particles of defined size and shape. By combining tracking of GEMs with genetic and pharmacological approaches, we discovered that the mTORC1 pathway can modulate the effective diffusion coefficient of particles ≥20 nm in diameter more than 2-fold by tuning ribosome concentration, without any discernable effect on the motion of molecules ≤5 nm. This change in ribosome concentration affected phase separation both in vitro and in vivo. Together, these results establish a role for mTORC1 in controlling both the mesoscale biophysical properties of the cytoplasm and biomolecular condensation.
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Affiliation(s)
- M Delarue
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G P Brittingham
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - S Pfeffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - I V Surovtsev
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA
| | - S Pinglay
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - K J Kennedy
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - M Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J I Gutierrez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 95720, USA
| | - D Sang
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - G Poterewicz
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA
| | - J K Chung
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA
| | - J M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - J T Groves
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 95720, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA
| | - C Jacobs-Wagner
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06511, USA; Howard Hughes Medical Institute, Chevy Chase, MD 20815, USA; Microbial Sciences Institute, Yale West Campus, West Haven, CT 06516, USA; Department of Microbial Pathogenesis, Yale School of Medicine, New Haven, CT 06511, USA
| | - B D Engel
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - L J Holt
- Institute for Systems Genetics, New York University Langone Health, New York, NY 10016, USA.
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27
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Braunger K, Pfeffer S, Shrimal S, Gilmore R, Berninghausen O, Mandon EC, Becker T, Förster F, Beckmann R. Structural basis for coupling protein transport and N-glycosylation at the mammalian endoplasmic reticulum. Science 2018. [PMID: 29519914 DOI: 10.1126/science.aar7899] [Citation(s) in RCA: 134] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Protein synthesis, transport, and N-glycosylation are coupled at the mammalian endoplasmic reticulum by complex formation of a ribosome, the Sec61 protein-conducting channel, and oligosaccharyltransferase (OST). Here we used different cryo-electron microscopy approaches to determine structures of native and solubilized ribosome-Sec61-OST complexes. A molecular model for the catalytic OST subunit STT3A (staurosporine and temperature sensitive 3A) revealed how it is integrated into the OST and how STT3-paralog specificity for translocon-associated OST is achieved. The OST subunit DC2 was placed at the interface between Sec61 and STT3A, where it acts as a versatile module for recruitment of STT3A-containing OST to the ribosome-Sec61 complex. This detailed structural view on the molecular architecture of the cotranslational machinery for N-glycosylation provides the basis for a mechanistic understanding of glycoprotein biogenesis at the endoplasmic reticulum.
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Affiliation(s)
- Katharina Braunger
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - Shiteshu Shrimal
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Reid Gilmore
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Otto Berninghausen
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany
| | - Elisabet C Mandon
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Thomas Becker
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, Netherlands.
| | - Roland Beckmann
- Department of Biochemistry, Gene Center and Center for Integrated Protein Science Munich, University of Munich, 81377 Munich, Germany.
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28
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Lang S, Pfeffer S, Lee PH, Cavalié A, Helms V, Förster F, Zimmermann R. An Update on Sec61 Channel Functions, Mechanisms, and Related Diseases. Front Physiol 2017; 8:887. [PMID: 29163222 PMCID: PMC5672155 DOI: 10.3389/fphys.2017.00887] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Accepted: 10/19/2017] [Indexed: 12/18/2022] Open
Abstract
The membrane of the endoplasmic reticulum (ER) of nucleated human cells harbors the protein translocon, which facilitates membrane integration or translocation of almost every newly synthesized polypeptide targeted to organelles of the endo- and exocytotic pathway. The translocon comprises the polypeptide-conducting Sec61 channel and several additional proteins and complexes that are permanently or transiently associated with the heterotrimeric Sec61 complex. This ensemble of proteins facilitates ER targeting of precursor polypeptides, modification of precursor polypeptides in transit through the Sec61 complex, and Sec61 channel gating, i.e., dynamic regulation of the pore forming subunit to mediate precursor transport and calcium efflux. Recently, cryoelectron tomography of translocons in native ER membrane vesicles, derived from human cell lines or patient fibroblasts, and even intact cells has given unprecedented insights into the architecture and dynamics of the native translocon and the Sec61 channel. These structural data are discussed in light of different Sec61 channel activities including ribosome receptor function, membrane insertion, and translocation of newly synthesized polypeptides as well as the putative physiological roles of the Sec61 channel as a passive ER calcium leak channel. Furthermore, the structural insights into the Sec61 channel are incorporated into an overview and update on Sec61 channel-related diseases—the Sec61 channelopathies—and novel therapeutic concepts for their treatment.
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Affiliation(s)
- Sven Lang
- Competence Center for Molecular Medicine, Saarland University Medical School, Homburg, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Martinsried, Germany
| | - Po-Hsien Lee
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Adolfo Cavalié
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, Homburg, Germany
| | - Volkhard Helms
- Center for Bioinformatics, Saarland University, Saarbrücken, Germany
| | - Friedrich Förster
- Bijvoet Center for Biomolecular Research, Utrecht University, Utrecht, Netherlands
| | - Richard Zimmermann
- Competence Center for Molecular Medicine, Saarland University Medical School, Homburg, Germany
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29
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Englmeier R, Pfeffer S, Förster F. Structure of the Human Mitochondrial Ribosome Studied In Situ by Cryoelectron Tomography. Structure 2017; 25:1574-1581.e2. [PMID: 28867615 DOI: 10.1016/j.str.2017.07.011] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Revised: 06/12/2017] [Accepted: 07/26/2017] [Indexed: 01/26/2023]
Abstract
Mitochondria maintain their own genome and its corresponding protein synthesis machine, the mitochondrial ribosome (mitoribosome). Mitoribosomes primarily synthesize highly hydrophobic proteins of the inner mitochondrial membrane. Recent studies revealed the complete structure of the isolated mammalian mitoribosome, but its mode of membrane association remained hypothetical. In this study, we used cryoelectron tomography to visualize human mitoribosomes in isolated mitochondria. The subtomogram average of the membrane-associated human mitoribosome reveals a single major contact site with the inner membrane, mediated by the mitochondria-specific protein mL45. A second rRNA-mediated contact site that is present in yeast is absent in humans, resulting in a more variable association of the human mitoribosome with the inner membrane. Despite extensive structural differences of mammalian and fungal mitoribosomal structure, the principal organization of peptide exit tunnel and the mL45 homolog remains invariant, presumably to align the mitoribosome with the membrane-embedded insertion machinery.
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Affiliation(s)
- Robert Englmeier
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Stefan Pfeffer
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, 82152 Martinsried, Germany
| | - Friedrich Förster
- Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, 82152 Martinsried, Germany.
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30
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Pfeffer S, Dudek J, Schaffer M, Ng BG, Albert S, Plitzko JM, Baumeister W, Zimmermann R, Freeze HH, Engel BD, Förster F. Dissecting the molecular organization of the translocon-associated protein complex. Nat Commun 2017; 8:14516. [PMID: 28218252 PMCID: PMC5321747 DOI: 10.1038/ncomms14516] [Citation(s) in RCA: 95] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/05/2017] [Indexed: 12/26/2022] Open
Abstract
In eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein (TRAP) complex is an integral component of the translocon, assisting the Sec61 protein-conducting channel by regulating signal sequence and transmembrane helix insertion in a substrate-dependent manner. Here we use cryo-electron tomography (CET) to study the structure of the native translocon in evolutionarily divergent organisms and disease-linked TRAP mutant fibroblasts from human patients. The structural differences detected by subtomogram analysis form a basis for dissecting the molecular organization of the TRAP complex. We assign positions to the four TRAP subunits within the complex, providing insights into their individual functions. The revealed molecular architecture of a central translocon component advances our understanding of membrane protein biogenesis and sheds light on the role of TRAP in human congenital disorders of glycosylation.
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Affiliation(s)
- Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Johanna Dudek
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Building 44, 66421 Homburg, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Bobby G Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Sahradha Albert
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Richard Zimmermann
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Building 44, 66421 Homburg, Germany
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.,Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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31
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Khoshouei M, Pfeffer S, Baumeister W, Förster F, Danev R. Subtomogram analysis using the Volta phase plate. J Struct Biol 2017; 197:94-101. [DOI: 10.1016/j.jsb.2016.05.009] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2016] [Revised: 05/06/2016] [Accepted: 05/24/2016] [Indexed: 10/21/2022]
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32
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Pfeffer S, Dudek J, Zimmermann R, Förster F. Organization of the native ribosome-translocon complex at the mammalian endoplasmic reticulum membrane. Biochim Biophys Acta Gen Subj 2016; 1860:2122-9. [PMID: 27373685 DOI: 10.1016/j.bbagen.2016.06.024] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Revised: 06/24/2016] [Accepted: 06/28/2016] [Indexed: 11/17/2022]
Abstract
BACKGROUND In eukaryotic cells, many proteins have to be transported across or inserted into the endoplasmic reticulum membrane during their biogenesis on the ribosome. This process is facilitated by the protein translocon, a highly dynamic multi-subunit membrane protein complex. SCOPE OF REVIEW The aim of this review is to summarize the current structural knowledge about protein translocon components in mammals. MAJOR CONCLUSIONS Various structural biology approaches have been used in synergy to characterize the translocon in recent years. X-ray crystallography and cryoelectron microscopy single particle analysis have yielded highly detailed insights into the structure and functional mechanism of the protein-conducting channel Sec61, which constitutes the functional core of the translocon. Cryoelectron tomography and subtomogram analysis have advanced our understanding of the overall structure, molecular organization and compositional heterogeneity of the translocon in a native membrane environment. Tomography densities at subnanometer resolution revealed an intricate network of interactions between the ribosome, Sec61 and accessory translocon components that assist in protein transport, membrane insertion and maturation. GENERAL SIGNIFICANCE The protein translocon is a gateway for approximately one third of all synthesized proteins and numerous human diseases are associated with malfunctioning of its components. Thus, detailed insights into the structure and molecular organization of the translocon will not only advance our understanding of membrane protein biogenesis in general, but they can potentially pave the way for novel therapeutic approaches against human diseases.
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Affiliation(s)
- Stefan Pfeffer
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, D-82152 Martinsried, Germany
| | - Johanna Dudek
- Saarland University, Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany
| | - Richard Zimmermann
- Saarland University, Medical Biochemistry and Molecular Biology, D-66421 Homburg, Germany.
| | - Friedrich Förster
- Max-Planck Institute of Biochemistry, Department of Molecular Structural Biology, D-82152 Martinsried, Germany; Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.
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33
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Kromke M, Palomino-Schätzlein M, Mayer H, Pfeffer S, Pineda-Lucena A, Luy B, Hausberg M, Muhle-Goll C. Profiling human blood serum metabolites by nuclear magnetic resonance spectroscopy: a comprehensive tool for the evaluation of hemodialysis efficiency. Transl Res 2016; 171:71-82.e1-9. [PMID: 26924041 DOI: 10.1016/j.trsl.2016.02.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2015] [Revised: 01/28/2016] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
Abstract
Hemodialysis remains the standard therapy to treat patients affected with end-stage renal disease by removing metabolites accumulated in blood plasma. The efficiency of hemodialysis is mainly monitored by urea clearance, which is routinely checked in clinical laboratory practice. However, there is mounting evidence that the clearance behavior of selected single metabolites is not sufficient to predict long-term outcome of treatment. To address this problem, we evaluated the potential of nuclear magnetic resonance spectroscopy for monitoring hemodialysis efficiency by comprehensive profiling of blood serum metabolites. We carried out a pilot study with a cohort of end-stage chronic kidney disease patients (n = 29), analyzing their serum prior and immediately after hemodialysis. To account for supposed variability in the accumulation of metabolites and efficiency of hemodialysis, patients' blood sera were repeatedly collected over a period of several months. Our results revealed that the metabolic profile in terms of concentrations varied considerably between patients but was comparably constant on the patient's level over the period of 4 months. Interestingly, also the individual clearance of the metabolites was characteristic for each patient. Thus, it is conceivable that the observed patient-dependent clearance patterns reflect to some extent the patients' long-term perspectives. We conclude that nuclear magnetic resonance spectroscopy is an optimal tool to complement traditional clinical methods based on a single variable, providing comprehensive and much more global information, which is crucial for patient evaluation and the development of improved treatments of kidney failure.
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Affiliation(s)
- Marika Kromke
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Karlsruhe, Germany
| | - Martina Palomino-Schätzlein
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Karlsruhe, Germany; Centro de Investigación Príncipe Felipe, Valencia, Spain
| | - Horst Mayer
- Städtisches Klinikum Karlsruhe, Karlsruhe, Germany
| | | | - Antonio Pineda-Lucena
- Centro de Investigación Príncipe Felipe, Valencia, Spain; Instituto de Investigación Sanitaria La Fe, Valencia, Spain
| | - Burkhard Luy
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Karlsruhe, Germany; Karlsruhe Institute of Technology, Institute for Biological Interfaces 4, Karlsruhe, Germany
| | | | - Claudia Muhle-Goll
- Karlsruhe Institute of Technology, Institute of Organic Chemistry, Karlsruhe, Germany; Karlsruhe Institute of Technology, Institute for Biological Interfaces 4, Karlsruhe, Germany.
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34
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Mahamid J, Pfeffer S, Schaffer M, Villa E, Danev R, Cuellar LK, Förster F, Hyman AA, Plitzko JM, Baumeister W. Visualizing the molecular sociology at the HeLa cell nuclear periphery. Science 2016; 351:969-72. [PMID: 26917770 DOI: 10.1126/science.aad8857] [Citation(s) in RCA: 353] [Impact Index Per Article: 44.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The molecular organization of eukaryotic nuclear volumes remains largely unexplored. Here we combined recent developments in cryo-electron tomography (cryo-ET) to produce three-dimensional snapshots of the HeLa cell nuclear periphery. Subtomogram averaging and classification of ribosomes revealed the native structure and organization of the cytoplasmic translation machinery. Analysis of a large dynamic structure-the nuclear pore complex-revealed variations detectable at the level of individual complexes. Cryo-ET was used to visualize previously elusive structures, such as nucleosome chains and the filaments of the nuclear lamina, in situ. Elucidation of the lamina structure provides insight into its contribution to metazoan nuclear stiffness.
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Affiliation(s)
- Julia Mahamid
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | - Stefan Pfeffer
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Miroslava Schaffer
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Elizabeth Villa
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany. Department of Chemistry and Biochemistry, University of California, San Diego, CA, USA
| | - Radostin Danev
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Luis Kuhn Cuellar
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Friedrich Förster
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany
| | - Jürgen M Plitzko
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Max Planck Institute of Biochemistry, Department of Molecular Structural Biology, Am Klopferspitz 18, 82152 Martinsried, Germany.
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Affiliation(s)
- Stefan Pfeffer
- a Department of Molecular Structural Biology , Max-Planck Institute of Biochemistry , Martinsried , Germany
| | - Friedrich Förster
- a Department of Molecular Structural Biology , Max-Planck Institute of Biochemistry , Martinsried , Germany
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Pfeffer S, Dudek J, Gogala M, Schorr S, Linxweiler J, Lang S, Becker T, Beckmann R, Zimmermann R, Förster F. Structure of the mammalian oligosaccharyl-transferase complex in the native ER protein translocon. Nat Commun 2015; 5:3072. [PMID: 24407213 DOI: 10.1038/ncomms4072] [Citation(s) in RCA: 115] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2013] [Accepted: 12/06/2013] [Indexed: 12/17/2022] Open
Abstract
In mammalian cells, proteins are typically translocated across the endoplasmic reticulum (ER) membrane in a co-translational mode by the ER protein translocon, comprising the protein-conducting channel Sec61 and additional complexes involved in nascent chain processing and translocation. As an integral component of the translocon, the oligosaccharyl-transferase complex (OST) catalyses co-translational N-glycosylation, one of the most common protein modifications in eukaryotic cells. Here we use cryoelectron tomography, cryoelectron microscopy single-particle analysis and small interfering RNA-mediated gene silencing to determine the overall structure, oligomeric state and position of OST in the native ER protein translocon of mammalian cells in unprecedented detail. The observed positioning of OST in close proximity to Sec61 provides a basis for understanding how protein translocation into the ER and glycosylation of nascent proteins are structurally coupled. The overall spatial organization of the native translocon, as determined here, serves as a reliable framework for further hypothesis-driven studies.
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Affiliation(s)
- Stefan Pfeffer
- 1] Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany [2]
| | - Johanna Dudek
- 1] Department of Medical Biochemistry and Molecular Biology, Saarland University, D-66421 Homburg, Germany [2]
| | - Marko Gogala
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, University of Munich, D-81377 Munich, Germany
| | - Stefan Schorr
- Department of Medical Biochemistry and Molecular Biology, Saarland University, D-66421 Homburg, Germany
| | - Johannes Linxweiler
- Department of Medical Biochemistry and Molecular Biology, Saarland University, D-66421 Homburg, Germany
| | - Sven Lang
- Department of Medical Biochemistry and Molecular Biology, Saarland University, D-66421 Homburg, Germany
| | - Thomas Becker
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, University of Munich, D-81377 Munich, Germany
| | - Roland Beckmann
- Gene Center and Center for integrated Protein Science Munich, Department of Biochemistry, University of Munich, D-81377 Munich, Germany
| | - Richard Zimmermann
- Department of Medical Biochemistry and Molecular Biology, Saarland University, D-66421 Homburg, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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Steinhilber B, Hoffmann S, Karlovic K, Pfeffer S, Maier T, Hallasheh O, Kruck S, Seibt R, Rieger M, Heidingsfeld M, Feuer R, Sawodny O, Rothmund R, Sievert KD. PD18-04 DEVELOPMENT OF AN ARM SUPPORT SYSTEM TO IMPROVE ERGONOMICS IN LAPAROSCOPIC SURGERY – STUDY DESIGN AND PROVISIONAL RESULTS. J Urol 2015. [DOI: 10.1016/j.juro.2015.02.689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Pfeffer S, Woellhaf MW, Herrmann JM, Förster F. Organization of the mitochondrial translation machinery studied in situ by cryoelectron tomography. Nat Commun 2015; 6:6019. [PMID: 25609543 DOI: 10.1038/ncomms7019] [Citation(s) in RCA: 100] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 12/02/2014] [Indexed: 11/09/2022] Open
Abstract
Whereas the structure and function of cytosolic ribosomes have been studied in great detail, we know surprisingly little about the structural basis of mitochondrial protein synthesis. Here we used cryoelectron tomography and subtomogram analysis to visualize mitoribosomes in isolated yeast mitochondria, avoiding perturbations during ribosomal purification. Most mitoribosomes reside in immediate proximity to the inner mitochondrial membrane, in line with their specialization in the synthesis of hydrophobic membrane proteins. The subtomogram average of membrane-associated mitoribosomes reveals two distinct membrane contact sites, formed by the 21S rRNA expansion segment 96-ES1 and the inner membrane protein Mba1. On the basis of our data, we further hypothesize that Mba1 is not just a passive mitoribosome receptor on the inner membrane, but that it spatially aligns mitoribosomes with the membrane insertion machinery. This study reveals detailed insights into the supramolecular organization of the mitochondrial translation machinery and its association with the inner membrane in translation-competent mitochondria.
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Affiliation(s)
- Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
| | - Michael W Woellhaf
- Cell Biology, University of Kaiserslautern, Erwin-Schrodinger-Strasse 13, 67663 Kaiserslautern, Germany
| | - Johannes M Herrmann
- Cell Biology, University of Kaiserslautern, Erwin-Schrodinger-Strasse 13, 67663 Kaiserslautern, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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Steinhilber B, Hoffmann S, Karlovic K, Pfeffer S, Maier T, Hallasheh O, Kruck S, Seibt R, Rieger MA, Heidingsfeld M, Feuer R, Sawodny O, Rothmund R, Sievert KD. Development of an arm support system to improve ergonomics in laparoscopic surgery: study design and provisional results. Surg Endosc 2014; 29:2851-8. [PMID: 25539690 PMCID: PMC4541700 DOI: 10.1007/s00464-014-3984-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2014] [Accepted: 11/04/2014] [Indexed: 12/05/2022]
Abstract
Background Laparoscopic surgery (LS) induces physical stress to the surgeon that is associated with an increased prevalence of musculoskeletal pain and injury in the shoulder–neck region. The aim of this research project is to develop an arm support system (ASsyst) that reduces physical stress and is applicable to various laparoscopic interventions and operation room settings. Methods A systematic approach to develop an ASsyst started in October 2012 consisting of five consecutive steps. In step 1, 14 laparoscopic interventions were observed using subjective and objective measures to determine key indicators for the conception of an ASsyst in LS. In step 2, an expert workshop was held to find and evaluate solutions to generate concepts for a support system based on the results of step 1 and general methods. During the third step, prototypes of ASsyst were tested in an experimental setting. Steps 4 and 5 are currently in process and include the final development of the ASsyst using the most promising concept for the evaluation during simulated LS. Results Increased levels of physical stress were found in LS. Asymmetric strains were common. Three prototypes of ASsyst emerged from step 1 and 2. These prototypes were a cable construction with a noose for the lower arm, a support from below the elbow and a pneumatic vest supporting the upper arm. The experimental testing of these prototypes demonstrated reduced physical stress when compared to the unsupported environment. The support from below the elbow seemed to be the most practical in terms of implementation in various operation room settings and acceptance by surgeons. Step 4 and 5 are still in process. Conclusions Ergonomic problems have been identified in LS that could be addressed by an ASsyst. The concept of supporting the elbow from below has been found to be the most promising approach.
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Affiliation(s)
- Benjamin Steinhilber
- Institute of Occupational and Social Medicine and Health Services Research, University Hospital Tübingen, Tübingen, Germany,
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Chen Y, Pfeffer S, Fernández J, Sorzano C, Förster F. Autofocused 3D Classification of Cryoelectron Subtomograms. Structure 2014; 22:1528-37. [DOI: 10.1016/j.str.2014.08.007] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/03/2014] [Accepted: 08/08/2014] [Indexed: 10/24/2022]
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Dudek J, Pfeffer S, Lee PH, Jung M, Cavalié A, Helms V, Förster F, Zimmermann R. Protein transport into the human endoplasmic reticulum. J Mol Biol 2014; 427:1159-75. [PMID: 24968227 DOI: 10.1016/j.jmb.2014.06.011] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2014] [Accepted: 06/11/2014] [Indexed: 12/22/2022]
Abstract
Protein transport into the endoplasmic reticulum (ER) is essential for all eukaryotic cells and evolutionary related to protein transport into and across the cytoplasmic membrane of eubacteria and archaea. It is based on amino-terminal signal peptides in the precursor polypeptides plus various transport components in cytosol plus ER and can occur either cotranslationally or posttranslationally. The two mechanisms merge at the heterotrimeric Sec61 complex in the ER membrane, which forms an aqueous polypeptide-conducting channel. Since the mammalian ER is also the main intracellular calcium storage organelle, the Sec61 complex is tightly regulated in its dynamics between the open and closed conformations by various ligands, such as precursor polypeptides at the cytosolic face and the Hsp70-type molecular chaperone BiP at the ER lumenal face (Hsp, heat shock protein). Furthermore, BiP binding to the incoming precursor polypeptide contributes to unidirectionality and efficiency of transport. Recent insights into the structural dynamics of the Sec61 complex and related complexes in eubacteria and archaea have various mechanistic and functional implications.
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Affiliation(s)
- Johanna Dudek
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | - Stefan Pfeffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Po-Hsien Lee
- Computational Biology, Saarland University, 66041 Saarbrücken, Germany
| | - Martin Jung
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany
| | - Adolfo Cavalié
- Experimental and Clinical Pharmacology and Toxicology, Saarland University, 66421 Homburg, Germany
| | - Volkhard Helms
- Computational Biology, Saarland University, 66041 Saarbrücken, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Richard Zimmermann
- Medical Biochemistry and Molecular Biology, Saarland University, 66421 Homburg, Germany.
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Pfeffer S, Hofmann A, Maier T, Rothmund R, Sievert KD, Seibt R, Rieger MA, Steinhilber B. Ergonomics of Selected Laparoscopic Procedures - Need for Action? BIOMED ENG-BIOMED TE 2013; 58 Suppl 1:/j/bmte.2013.58.issue-s1-J/bmt-2013-4228/bmt-2013-4228.xml. [PMID: 24042889 DOI: 10.1515/bmt-2013-4228] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Namer B, Pfeffer S, Handwerker HO, Schmelz M, Bickel A. Axon reflex flare and quantitative sudomotor axon reflex contribute in the diagnosis of small fiber neuropathy. Muscle Nerve 2012. [DOI: 10.1002/mus.23543] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Barbara Namer
- Department of Physiology and Pathophysiology; University of Erlangen; Universitätsstr. 17, 91054 Erlangen Germany
| | - Stefan Pfeffer
- Department of Neurology; Friedrich-Alexander University Erlangen; Germany
| | - Hermann O. Handwerker
- Department of Physiology and Pathophysiology; University of Erlangen; Universitätsstr. 17, 91054 Erlangen Germany
| | - Martin Schmelz
- Department of Anesthesiology; Mannheim, University Heidelberg; Germany
| | - Andreas Bickel
- Department of Neurology; Friedrich-Alexander University Erlangen; Germany
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Pfeffer S, Brandt F, Hrabe T, Lang S, Eibauer M, Zimmermann R, Förster F. Structure and 3D arrangement of endoplasmic reticulum membrane-associated ribosomes. Structure 2012; 20:1508-18. [PMID: 22819217 DOI: 10.1016/j.str.2012.06.010] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Revised: 05/14/2012] [Accepted: 06/11/2012] [Indexed: 12/22/2022]
Abstract
In eukaryotic cells, cotranslational protein translocation across the endoplasmic reticulum (ER) membrane requires an elaborate macromolecular machinery. While structural details of ribosomes bound to purified and solubilized constituents of the translocon have been elucidated in recent years, little structural knowledge of ribosomes bound to the complete ER protein translocation machinery in a native membrane environment exists. Here, we used cryoelectron tomography to provide a three-dimensional reconstruction of 80S ribosomes attached to functional canine pancreatic ER microsomes in situ. In the resulting subtomogram average at 31 Å resolution, we observe direct contact of ribosomal expansion segment ES27L and the membrane and distinguish several membrane-embedded and lumenal complexes, including Sec61, the TRAP complex and another large complex protruding 90 Å into the lumen. Membrane-associated ribosomes adopt a preferred three-dimensional arrangement that is likely specific for ER-associated polyribosomes and may explain the high translation efficiency of ER-associated ribosomes compared to their cytosolic counterparts.
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Affiliation(s)
- Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, D-82152 Martinsried, Germany
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Stricker E, Pfeffer S, Trick M, Rall M, Maier T. Standardized research on ergonomics, usability and workflow analysis using high fidelity simulation labs. BIOMED ENG-BIOMED TE 2012. [DOI: 10.1515/bmt-2012-4285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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Hrabe T, Chen Y, Pfeffer S, Cuellar LK, Mangold AV, Förster F. PyTom: a python-based toolbox for localization of macromolecules in cryo-electron tomograms and subtomogram analysis. J Struct Biol 2011; 178:177-88. [PMID: 22193517 DOI: 10.1016/j.jsb.2011.12.003] [Citation(s) in RCA: 147] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/25/2011] [Accepted: 12/05/2011] [Indexed: 10/14/2022]
Abstract
Cryo-electron tomography (CET) is a three-dimensional imaging technique for structural studies of macromolecules under close-to-native conditions. In-depth analysis of macromolecule populations depicted in tomograms requires identification of subtomograms corresponding to putative particles, averaging of subtomograms to enhance their signal, and classification to capture the structural variations among them. Here, we introduce the open-source platform PyTom that unifies standard tomogram processing steps in a python toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies. Furthermore, we present a novel stochastic classification method that yields significantly more accurate classification results than two deterministic approaches in simulations. We demonstrate that the PyTom workflow yields faithful results for alignment and classification of simulated and experimental subtomograms of ribosomes and GroEL(14)/GroEL(14)GroES(7), respectively, as well as for the analysis of ribosomal 60S subunits in yeast cell lysate. PyTom enables parallelized processing of large numbers of tomograms, but also provides a convenient, sustainable environment for algorithmic development.
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Affiliation(s)
- Thomas Hrabe
- Max-Planck Institute of Biochemistry, Am Klopferspitz 18, D-82152 Martinsried, Germany
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Pfeffer S, Baumert T. Impact of microRNAs for pathogenesis and treatment of hepatitis C virus infection. ACTA ACUST UNITED AC 2010; 34:431-5. [DOI: 10.1016/j.gcb.2010.04.010] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 04/08/2010] [Indexed: 12/11/2022]
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Fratzl-Zelman N, Roschger P, Misof BM, Pfeffer S, Glorieux FH, Klaushofer K, Rauch F. Normative data on mineralization density distribution in iliac bone biopsies of children, adolescents and young adults. Bone 2009; 44:1043-8. [PMID: 19268565 DOI: 10.1016/j.bone.2009.02.021] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/22/2008] [Revised: 02/15/2009] [Accepted: 02/19/2009] [Indexed: 11/19/2022]
Abstract
Bone mineralization density distribution (BMDD) as assessed by quantitative backscattered electron imaging (qBEI) in iliac crest bone biopsies has become in the last years a powerful diagnostic tool to evaluate the effect of metabolic bone diseases and/or therapeutic interventions on the mineralization status of the bone material. However until now, normative reference data are only available for adults. The aim of the present study is to close this gap and establish normative data from children and compare them with reference BMDD data of adults. qBEI analyses were performed on bone samples from 54 individuals between 1.5 and 23 years without metabolic bone diseases, which were previously used as study population to establish normative histomorphometric standards. In the trabecular compartment, none of the BMDD parameters showed a significant correlation with age. The BMDD was shifted towards lower mineralization density (CaMean -5.6%, p<0.0001; CaPeak -5.6%, p<0.0001; CaLow +39.0% p<0.001; CaHigh -80.7%, p<0.001) and the inter-individual variation was higher compared to the adult population. The cortices appeared to be markedly less mineralized (CaMean -3.1%, p<0.0001) than cancellous bone due to higher amounts of low mineralized secondary bone. However, the cortical BMDD parameters showed a strong correlation (r=0.38 to 0.85, with p<0.001 to<0.0001) with cancellous BMDD parameters. In conclusion, this study provides evidence that BMDD parameters in growing healthy subjects are relatively constant and that these data can be used as normative references in pediatrics osteology. The larger inter-individual variability compared to adults is most likely related to alterations of the bone turnover rate during growth.
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Affiliation(s)
- N Fratzl-Zelman
- Ludwig Boltzmann Institute of Osteology, Hanusch Hospital of WGKK and AUVA Trauma Centre Meidling, 4th Med. Department, Hanusch Hospital, Heinrich Collin Str. 30, 1140 Vienna, Austria.
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Pfeffer S. [MicroRNAs and viral infections]. Virologie (Montrouge) 2007; 11:207-216. [PMID: 37012848 DOI: 10.1684/vir.2011.7731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/05/2023]
Abstract
RNA silencing plays an important role in development through the action of micro (mi) RNAs that fine tune the expression of a large portion of the genome. But, in plants and insects, it is also a very important player in innate immune responses, especially in antiviral defense. It is now well established that the RNA silencing machinery targets plant as well as insect viruses. As the genetic basis underlying this defense mechanism in these organisms starts being elucidated, much less is known about the possible antiviral role ofRNAsilencing in mammals. No small interferingRNAs (siRNAs) of viral origin can be detected in human cells infected withRNAviruses. On the contrary, viral smallRNAs can be found in cells infected by the DNA virus Epstein-Barr, but they rather resemble miRNAs. This primary observation has been extended to other members of the herpesvirus family as well as other DNA viruses such as the polyomavirus SV40. These findings indicate that, rather than being targeted by RNA silencing, human DNA viruses seem to have evolved their own miRNAs to modulate the expression of their own genes or of their host's.
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Affiliation(s)
- S Pfeffer
- Institut de biologie moléculaire des plantes, laboratoire propre du CNRS (UPR 2357) conventionné avec l'Université Louis-Pasteur, 12, rue du Général-Zimmer, 67084 Strasbourg Cedex, France
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