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Brito Querido J, Sokabe M, Díaz-López I, Gordiyenko Y, Zuber P, Du Y, Albacete-Albacete L, Ramakrishnan V, Fraser CS. Human tumor suppressor protein Pdcd4 binds at the mRNA entry channel in the 40S small ribosomal subunit. Nat Commun 2024; 15:6633. [PMID: 39117603 PMCID: PMC11310195 DOI: 10.1038/s41467-024-50672-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2023] [Accepted: 07/17/2024] [Indexed: 08/10/2024] Open
Abstract
Translation is regulated mainly in the initiation step, and its dysregulation is implicated in many human diseases. Several proteins have been found to regulate translational initiation, including Pdcd4 (programmed cell death gene 4). Pdcd4 is a tumor suppressor protein that prevents cell growth, invasion, and metastasis. It is downregulated in most tumor cells, while global translation in the cell is upregulated. To understand the mechanisms underlying translational control by Pdcd4, we used single-particle cryo-electron microscopy to determine the structure of human Pdcd4 bound to 40S small ribosomal subunit, including Pdcd4-40S and Pdcd4-40S-eIF4A-eIF3-eIF1 complexes. The structures reveal the binding site of Pdcd4 at the mRNA entry site in the 40S, where the C-terminal domain (CTD) interacts with eIF4A at the mRNA entry site, while the N-terminal domain (NTD) is inserted into the mRNA channel and decoding site. The structures, together with quantitative binding and in vitro translation assays, shed light on the critical role of the NTD for the recruitment of Pdcd4 to the ribosomal complex and suggest a model whereby Pdcd4 blocks the eIF4F-independent role of eIF4A during recruitment and scanning of the 5' UTR of mRNA.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge, UK.
- Department of Biological Chemistry, University of Michigan, Ann Arbor, MI, USA.
- Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA.
- Center for RNA Biomedicine, University of Michigan, Ann Arbor, MI, USA.
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | | | | | | | - Yifei Du
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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2
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Brito Querido J, Sokabe M, Díaz-López I, Gordiyenko Y, Fraser CS, Ramakrishnan V. The structure of a human translation initiation complex reveals two independent roles for the helicase eIF4A. Nat Struct Mol Biol 2024; 31:455-464. [PMID: 38287194 PMCID: PMC10948362 DOI: 10.1038/s41594-023-01196-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 11/30/2023] [Indexed: 01/31/2024]
Abstract
Eukaryotic translation initiation involves recruitment of the 43S pre-initiation complex to the 5' end of mRNA by the cap-binding complex eIF4F, forming the 48S translation initiation complex (48S), which then scans along the mRNA until the start codon is recognized. We have previously shown that eIF4F binds near the mRNA exit channel of the 43S, leaving open the question of how mRNA secondary structure is removed as it enters the mRNA channel on the other side of the 40S subunit. Here we report the structure of a human 48S that shows that, in addition to the eIF4A that is part of eIF4F, there is a second eIF4A helicase bound at the mRNA entry site, which could unwind RNA secondary structures as they enter the 48S. The structure also reveals conserved interactions between eIF4F and the 43S, probaby explaining how eIF4F can promote mRNA recruitment in all eukaryotes.
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Affiliation(s)
- Jailson Brito Querido
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Biological Chemistry and Life Sciences Institute, University of Michigan, Ann Arbor, MI, USA
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | | | | | - Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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3
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Parkhurst JM, Cavalleri A, Dumoux M, Basham M, Clare D, Siebert CA, Evans G, Naismith JH, Kirkland A, Essex JW. Computational models of amorphous ice for accurate simulation of cryo-EM images of biological samples. Ultramicroscopy 2024; 256:113882. [PMID: 37979542 PMCID: PMC10730944 DOI: 10.1016/j.ultramic.2023.113882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 10/18/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
Simulations of cryo-electron microscopy (cryo-EM) images of biological samples can be used to produce test datasets to support the development of instrumentation, methods, and software, as well as to assess data acquisition and analysis strategies. To be useful, these simulations need to be based on physically realistic models which include large volumes of amorphous ice. The gold standard model for EM image simulation is a physical atom-based ice model produced using molecular dynamics simulations. Although practical for small sample volumes; for simulation of cryo-EM data from large sample volumes, this can be too computationally expensive. We have evaluated a Gaussian Random Field (GRF) ice model which is shown to be more computationally efficient for large sample volumes. The simulated EM images are compared with the gold standard atom-based ice model approach and shown to be directly comparable. Comparison with experimentally acquired data shows the Gaussian random field ice model produces realistic simulations. The software required has been implemented in the Parakeet software package and the underlying atomic models are available online for use by the wider community.
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Affiliation(s)
- James M Parkhurst
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom.
| | - Anna Cavalleri
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
| | - Maud Dumoux
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom
| | - Mark Basham
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Daniel Clare
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - C Alistair Siebert
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - Gwyndaf Evans
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom
| | - James H Naismith
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom; Division of Structural Biology, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, United Kingdom
| | - Angus Kirkland
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot, OX11 0FA, United Kingdom; Diamond Light Source, Harwell Science and Innovation Campus, Didcot, OX11 0DE, United Kingdom; Department of Materials, University of Oxford, Parks Road, Oxford, OX1 3PH, United Kingdom
| | - Jonathan W Essex
- School of Chemistry, University of Southampton, Highfield, Southampton, SO17 1BJ, United Kingdom
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4
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Dickerson JL, Leahy E, Peet MJ, Naydenova K, Russo CJ. Accurate magnification determination for cryoEM using gold. Ultramicroscopy 2024; 256:113883. [PMID: 38008055 PMCID: PMC10782223 DOI: 10.1016/j.ultramic.2023.113883] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 10/27/2023] [Accepted: 11/07/2023] [Indexed: 11/28/2023]
Abstract
Determining the correct magnified pixel size of single-particle cryoEM micrographs is necessary to maximize resolution and enable accurate model building. Here we describe a simple and rapid procedure for determining the absolute magnification in an electron cryomicroscope to a precision of <0.5%. We show how to use the atomic lattice spacings of crystals of thin and readily available test specimens, such as gold, as an absolute reference to determine magnification for both room temperature and cryogenic imaging. We compare this method to other commonly used methods, and show that it provides comparable accuracy in spite of its simplicity. This magnification calibration method provides a definitive reference quantity for data analysis and processing, simplifies the combination of multiple datasets from different microscopes and detectors, and improves the accuracy with which the contrast transfer function of the microscope can be determined. We also provide an open source program, magCalEM, which can be used to accurately estimate the magnified pixel size of a cryoEM dataset ex post facto.
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Affiliation(s)
- Joshua L Dickerson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Erin Leahy
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Mathew J Peet
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Katerina Naydenova
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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5
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Muir KW, Batters C, Dendooven T, Yang J, Zhang Z, Burt A, Barford D. Structural mechanism of outer kinetochore Dam1-Ndc80 complex assembly on microtubules. Science 2023; 382:1184-1190. [PMID: 38060647 PMCID: PMC7615550 DOI: 10.1126/science.adj8736] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Accepted: 10/25/2023] [Indexed: 12/18/2023]
Abstract
Kinetochores couple chromosomes to the mitotic spindle to segregate the genome during cell division. An error correction mechanism drives the turnover of kinetochore-microtubule attachments until biorientation is achieved. The structural basis for how kinetochore-mediated chromosome segregation is accomplished and regulated remains an outstanding question. In this work, we describe the cryo-electron microscopy structure of the budding yeast outer kinetochore Ndc80 and Dam1 ring complexes assembled onto microtubules. Complex assembly occurs through multiple interfaces, and a staple within Dam1 aids ring assembly. Perturbation of key interfaces suppresses yeast viability. Force-rupture assays indicated that this is a consequence of impaired kinetochore-microtubule attachment. The presence of error correction phosphorylation sites at Ndc80-Dam1 ring complex interfaces and the Dam1 staple explains how kinetochore-microtubule attachments are destabilized and reset.
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Affiliation(s)
- Kyle W. Muir
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Christopher Batters
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Tom Dendooven
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Jing Yang
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Ziguo Zhang
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - Alister Burt
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
| | - David Barford
- MRC Laboratory of Molecular Biology; Francis Crick Avenue, Cambridge, CB2 0QH, UK
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6
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McMullan G, Naydenova K, Mihaylov D, Yamashita K, Peet MJ, Wilson H, Dickerson JL, Chen S, Cannone G, Lee Y, Hutchings KA, Gittins O, Sobhy MA, Wells T, El-Gomati MM, Dalby J, Meffert M, Schulze-Briese C, Henderson R, Russo CJ. Structure determination by cryoEM at 100 keV. Proc Natl Acad Sci U S A 2023; 120:e2312905120. [PMID: 38011573 PMCID: PMC10710074 DOI: 10.1073/pnas.2312905120] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Accepted: 10/02/2023] [Indexed: 11/29/2023] Open
Abstract
Electron cryomicroscopy can, in principle, determine the structures of most biological molecules but is currently limited by access, specimen preparation difficulties, and cost. We describe a purpose-built instrument operating at 100 keV-including advances in electron optics, detection, and processing-that makes structure determination fast and simple at a fraction of current costs. The instrument attains its theoretical performance limits, allowing atomic resolution imaging of gold test specimens and biological molecular structure determination in hours. We demonstrate its capabilities by determining the structures of eleven different specimens, ranging in size from 140 kDa to 2 MDa, using a fraction of the data normally required. CryoEM with a microscope designed specifically for high-efficiency, on-the-spot imaging of biological molecules will expand structural biology to a wide range of previously intractable problems.
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Affiliation(s)
- Greg McMullan
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Katerina Naydenova
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Daniel Mihaylov
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Keitaro Yamashita
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Mathew J. Peet
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Hugh Wilson
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Joshua L. Dickerson
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Shaoxia Chen
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Giuseppe Cannone
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Yang Lee
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Katherine A. Hutchings
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Olivia Gittins
- Newcastle University, Newcastle upon TyneNE2 4HH, United Kingdom
| | - Mohamed A. Sobhy
- King Abdullah University of Science and Technology, Thuwal23955, Saudi Arabia
| | - Torquil Wells
- York Probe Sources Ltd., YorkYO26 6QU, United Kingdom
| | | | - Jason Dalby
- JEOL U.K. Ltd., Welwyn Garden CityAL7 1LT, United Kingdom
| | | | | | - Richard Henderson
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
| | - Christopher J. Russo
- Medical Research Council (MRC) Laboratory of Molecular Biology, CambridgeCB2 0QH, United Kingdom
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7
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Wozny MR, Di Luca A, Morado DR, Picco A, Khaddaj R, Campomanes P, Ivanović L, Hoffmann PC, Miller EA, Vanni S, Kukulski W. In situ architecture of the ER-mitochondria encounter structure. Nature 2023:10.1038/s41586-023-06050-3. [PMID: 37165187 DOI: 10.1038/s41586-023-06050-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Accepted: 04/04/2023] [Indexed: 05/12/2023]
Abstract
The endoplasmic reticulum and mitochondria are main hubs of eukaryotic membrane biogenesis that rely on lipid exchange via membrane contact sites1-3, but the underpinning mechanisms remain poorly understood. In yeast, tethering and lipid transfer between the two organelles is mediated by the endoplasmic reticulum-mitochondria encounter structure (ERMES), a four-subunit complex of unresolved stoichiometry and architecture4-6. Here we determined the molecular organization of ERMES within Saccharomyces cerevisiae cells using integrative structural biology by combining quantitative live imaging, cryo-correlative microscopy, subtomogram averaging and molecular modelling. We found that ERMES assembles into approximately 25 discrete bridge-like complexes distributed irregularly across a contact site. Each bridge consists of three synaptotagmin-like mitochondrial lipid binding protein domains oriented in a zig-zag arrangement. Our molecular model of ERMES reveals a pathway for lipids. These findings resolve the in situ supramolecular architecture of a major inter-organelle lipid transfer machinery and provide a basis for the mechanistic understanding of lipid fluxes in eukaryotic cells.
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Affiliation(s)
- Michael R Wozny
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Department of Anatomy and Cell Biology, McGill University, Montreal, Quebec, Canada
| | - Andrea Di Luca
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Dustin R Morado
- MRC Laboratory of Molecular Biology, Cambridge, UK
- SciLifeLab, Solna, Sweden
- Max Planck Institute of Biochemistry, Martinsried, Germany
| | - Andrea Picco
- Department of Biochemistry, University of Geneva, Geneva, Switzerland
| | - Rasha Khaddaj
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
| | - Pablo Campomanes
- Department of Biology, University of Fribourg, Fribourg, Switzerland
| | - Lazar Ivanović
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Patrick C Hoffmann
- MRC Laboratory of Molecular Biology, Cambridge, UK
- Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | | | - Stefano Vanni
- Department of Biology, University of Fribourg, Fribourg, Switzerland.
| | - Wanda Kukulski
- MRC Laboratory of Molecular Biology, Cambridge, UK.
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bern, Switzerland.
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8
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Wagstaff JM, Planelles-Herrero VJ, Sharov G, Alnami A, Kozielski F, Derivery E, Löwe J. Diverse cytomotive actins and tubulins share a polymerization switch mechanism conferring robust dynamics. SCIENCE ADVANCES 2023; 9:eadf3021. [PMID: 36989372 PMCID: PMC10058229 DOI: 10.1126/sciadv.adf3021] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2022] [Accepted: 03/01/2023] [Indexed: 06/19/2023]
Abstract
Protein filaments are used in myriads of ways to organize other molecules within cells. Some filament-forming proteins couple the hydrolysis of nucleotides to their polymerization cycle, thus powering the movement of other molecules. These filaments are termed cytomotive. Only members of the actin and tubulin protein superfamilies are known to form cytomotive filaments. We examined the basis of cytomotivity via structural studies of the polymerization cycles of actin and tubulin homologs from across the tree of life. We analyzed published data and performed structural experiments designed to disentangle functional components of these complex filament systems. Our analysis demonstrates the existence of shared subunit polymerization switches among both cytomotive actins and tubulins, i.e., the conformation of subunits switches upon assembly into filaments. These cytomotive switches can explain filament robustness, by enabling the coupling of kinetic and structural polarities required for cytomotive behaviors and by ensuring that single cytomotive filaments do not fall apart.
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Affiliation(s)
- James Mark Wagstaff
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | | | - Grigory Sharov
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Aisha Alnami
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Frank Kozielski
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Emmanuel Derivery
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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9
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Hurtig F, Burgers TC, Cezanne A, Jiang X, Mol FN, Traparić J, Pulschen AA, Nierhaus T, Tarrason-Risa G, Harker-Kirschneck L, Löwe J, Šarić A, Vlijm R, Baum B. The patterned assembly and stepwise Vps4-mediated disassembly of composite ESCRT-III polymers drives archaeal cell division. SCIENCE ADVANCES 2023; 9:eade5224. [PMID: 36921039 PMCID: PMC10017037 DOI: 10.1126/sciadv.ade5224] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 02/14/2023] [Indexed: 05/13/2023]
Abstract
ESCRT-III family proteins form composite polymers that deform and cut membrane tubes in the context of a wide range of cell biological processes across the tree of life. In reconstituted systems, sequential changes in the composition of ESCRT-III polymers induced by the AAA-adenosine triphosphatase Vps4 have been shown to remodel membranes. However, it is not known how composite ESCRT-III polymers are organized and remodeled in space and time in a cellular context. Taking advantage of the relative simplicity of the ESCRT-III-dependent division system in Sulfolobus acidocaldarius, one of the closest experimentally tractable prokaryotic relatives of eukaryotes, we use super-resolution microscopy, electron microscopy, and computational modeling to show how CdvB/CdvB1/CdvB2 proteins form a precisely patterned composite ESCRT-III division ring, which undergoes stepwise Vps4-dependent disassembly and contracts to cut cells into two. These observations lead us to suggest sequential changes in a patterned composite polymer as a general mechanism of ESCRT-III-dependent membrane remodeling.
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Affiliation(s)
- Fredrik Hurtig
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Thomas C. Q. Burgers
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
| | - Alice Cezanne
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Xiuyun Jiang
- Laboratory of Soft Matter Physics, The Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Frank N. Mol
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
| | - Jovan Traparić
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Tim Nierhaus
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | | | - Lena Harker-Kirschneck
- University College London, Institute for the Physics of Living Systems, WC1E 6BT London, UK
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
| | - Anđela Šarić
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
| | - Rifka Vlijm
- Molecular Biophysics, Zernike Institute for Advanced Materials, University of Groningen, 9747 AG Groningen, Netherlands
| | - Buzz Baum
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
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10
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Ganeva I, Lim K, Boulanger J, Hoffmann PC, Muriel O, Borgeaud AC, Hagen WJH, Savage DB, Kukulski W. The architecture of Cidec-mediated interfaces between lipid droplets. Cell Rep 2023; 42:112107. [PMID: 36800289 PMCID: PMC9989828 DOI: 10.1016/j.celrep.2023.112107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/14/2022] [Accepted: 01/30/2023] [Indexed: 02/18/2023] Open
Abstract
Lipid droplets (LDs) are intracellular organelles responsible for storing surplus energy as neutral lipids. Their size and number vary enormously. In white adipocytes, LDs can reach 100 μm in diameter, occupying >90% of the cell. Cidec, which is strictly required for the formation of large LDs, is concentrated at interfaces between adjacent LDs and facilitates directional flux of neutral lipids from the smaller to the larger LD. The mechanism of lipid transfer is unclear, in part because the architecture of interfaces between LDs remains elusive. Here we visualize interfaces between LDs by electron cryo-tomography and analyze the kinetics of lipid transfer by quantitative live fluorescence microscopy. We show that transfer occurs through closely apposed monolayers, is slowed down by increasing the distance between the monolayers, and follows exponential kinetics. Our data corroborate the notion that Cidec facilitates pressure-driven transfer of neutral lipids through two "leaky" monolayers between LDs.
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Affiliation(s)
- Iva Ganeva
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Koini Lim
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK
| | - Jerome Boulanger
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Patrick C Hoffmann
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Olivia Muriel
- Electron Microscopy Facility, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland; Department of Fundamental Microbiology, Faculty of Biology and Medicine, University of Lausanne, Biophore Building, 1015 Lausanne, Switzerland
| | - Alicia C Borgeaud
- Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland
| | - Wim J H Hagen
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany
| | - David B Savage
- Metabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Wanda Kukulski
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK; Institute of Biochemistry and Molecular Medicine, University of Bern, Bühlstrasse 28, 3012 Bern, Switzerland.
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11
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Nierhaus T, McLaughlin SH, Bürmann F, Kureisaite-Ciziene D, Maslen SL, Skehel JM, Yu CWH, Freund SMV, Funke LFH, Chin JW, Löwe J. Bacterial divisome protein FtsA forms curved antiparallel double filaments when binding to FtsN. Nat Microbiol 2022; 7:1686-1701. [PMID: 36123441 PMCID: PMC7613929 DOI: 10.1038/s41564-022-01206-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/19/2022] [Indexed: 11/08/2022]
Abstract
During bacterial cell division, filaments of tubulin-like FtsZ form the Z-ring, which is the cytoplasmic scaffold for divisome assembly. In Escherichia coli, the actin homologue FtsA anchors the Z-ring to the membrane and recruits divisome components, including bitopic FtsN. FtsN regulates the periplasmic peptidoglycan synthase FtsWI. To characterize how FtsA regulates FtsN, we applied electron microscopy to show that E. coli FtsA forms antiparallel double filaments on lipid monolayers when bound to the cytoplasmic tail of FtsN. Using X-ray crystallography, we demonstrate that Vibrio maritimus FtsA crystallizes as an equivalent double filament. We identified an FtsA-FtsN interaction site in the IA-IC interdomain cleft of FtsA using X-ray crystallography and confirmed that FtsA forms double filaments in vivo by site-specific cysteine cross-linking. FtsA-FtsN double filaments reconstituted in or on liposomes prefer negative Gaussian curvature, like those of MreB, the actin-like protein of the elongasome. We propose that curved antiparallel FtsA double filaments together with treadmilling FtsZ filaments organize septal peptidoglycan synthesis in the division plane.
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Affiliation(s)
- Tim Nierhaus
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | | | - Sarah L Maslen
- MRC Laboratory of Molecular Biology, Cambridge, UK
- The Francis Crick Institute, London, UK
| | - J Mark Skehel
- MRC Laboratory of Molecular Biology, Cambridge, UK
- The Francis Crick Institute, London, UK
| | - Conny W H Yu
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | | | | | - Jason W Chin
- MRC Laboratory of Molecular Biology, Cambridge, UK
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, UK.
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12
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Lee BG, Rhodes J, Löwe J. Clamping of DNA shuts the condensin neck gate. Proc Natl Acad Sci U S A 2022; 119:e2120006119. [PMID: 35349345 PMCID: PMC9168836 DOI: 10.1073/pnas.2120006119] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 02/24/2022] [Indexed: 01/05/2023] Open
Abstract
SignificanceDNA needs to be compacted to fit into nuclei and during cell division, when dense chromatids are formed for their mechanical segregation, a process that depends on the protein complex condensin. It forms and enlarges loops in DNA through loop extrusion. Our work resolves the atomic structure of a DNA-bound state of condensin in which ATP has not been hydrolyzed. The DNA is clamped within a compartment that has been reported previously in other structural maintenance of chromosomes (SMC) complexes, including Rad50, cohesin, and MukBEF. With the caveat of important differences, it means that all SMC complexes cycle through at least some similar states and undergo similar conformational changes in their head modules, while hydrolyzing ATP and translocating DNA.
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Affiliation(s)
- Byung-Gil Lee
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - James Rhodes
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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13
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Pilsl M, Heiss FB, Pöll G, Höcherl M, Milkereit P, Engel C. Preparation of RNA Polymerase Complexes for Their Analysis by Single-Particle Cryo-Electron Microscopy. Methods Mol Biol 2022; 2533:81-96. [PMID: 35796984 PMCID: PMC9761500 DOI: 10.1007/978-1-0716-2501-9_6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Recent technological progress revealed new prospects of high-resolution structure determination of macromolecular complexes using cryo-electron microscopy (cryo-EM) . In the field of RNA polymerase (Pol) I research, a number of cryo-EM studies contributed to understanding the highly specialized mechanisms underlying the transcription of ribosomal RNA genes . Despite a broad applicability of the cryo-EM method itself, preparation of samples for high-resolution data collection can be challenging. Here, we describe strategies for the purification and stabilization of Pol I complexes, exemplarily considering advantages and disadvantages of the methodology. We further provide an easy-to-implement protocol for the coating of EM-grids with self-made carbon support films. In sum, we present an efficient workflow for cryo-grid preparation and optimization, including early stage cryo-EM screening that can be adapted to a wide range of soluble samples for high-resolution structure determination .
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Affiliation(s)
- Michael Pilsl
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Florian B Heiss
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Gisela Pöll
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Mona Höcherl
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Philipp Milkereit
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany
| | - Christoph Engel
- Regensburg Center for Biochemistry (RCB), University of Regensburg, Regensburg, Germany.
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14
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Integrated wafer-scale manufacturing of electron cryomicroscopy specimen supports. Ultramicroscopy 2022; 232:113396. [PMID: 34740028 PMCID: PMC8689146 DOI: 10.1016/j.ultramic.2021.113396] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2021] [Accepted: 09/20/2021] [Indexed: 12/31/2022]
Abstract
We present a process for the manufacture of electron cryomicroscopy (cryoEM) specimen supports with an integrated foil-grid structure, using cryogenic vacuum evaporation (cryoEvap) and patterned electroplating on a silicon wafer substrate. The process is designed to produce a pattern of nanometre scale holes in a thin metal foil, which is attached to a pattern of micrometre scale grid bars that support it and allow handling of the millimetre scale device. All steps are carried out on a single 4 inch (100 mm) silicon wafer, without any need to handle individual grids during processing, and yield about 600 supports per wafer. The approach is generally applicable to the problem of creating a thin foil with nanometre scale features and a micrometre scale support structure; here it is used to make an all gold, HexAuFoil type design. It also allows for the addition of custom fiducial markers and patterns which aid in locating and identifying particular regions of a grid at several length scales: by eye, in an optical microscope, and in the electron microscope. Implemented at scale, this manufacturing process can supply ample grids to support the continued growth of cryoEM for determining the structure of biological molecules.
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15
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Singewald K, Wilkinson JA, Saxena AS. Copper Based Site-directed Spin Labeling of Proteins for Use in Pulsed and Continuous Wave EPR Spectroscopy. Bio Protoc 2021; 11:e4258. [PMID: 35087917 DOI: 10.21769/bioprotoc.4258] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 10/08/2021] [Accepted: 10/13/2021] [Indexed: 11/02/2022] Open
Abstract
Site-directed spin labeling in conjunction with electron paramagnetic resonance (EPR) is an attractive approach to measure residue specific dynamics and point-to-point distance distributions in a biomolecule. Here, we focus on the labeling of proteins with a Cu(II)-nitrilotriacetic acid (NTA) complex, by exploiting two strategically placed histidine residues (called the dHis motif). This labeling strategy has emerged as a means to overcome key limitations of many spin labels. Through utilizing the dHis motif, Cu(II)NTA rigidly binds to a protein without depending on cysteine residues. This protocol outlines three major points: the synthesis of the Cu(II)NTA complex; the measurement of continuous wave and pulsed EPR spectra, to verify a successful synthesis, as well as successful protein labeling; and utilizing Cu(II)NTA labeled proteins, to measure distance constraints and backbone dynamics. In doing so, EPR measurements are less influenced by sidechain motion, which influences the breadth of the measured distance distributions between two spins, as well as the measured residue-specific dynamics. More broadly, such EPR-based distance measurements provide unique structural constraints for integrative structural biophysics and complement traditional biophysical techniques, such as NMR, cryo-EM, FRET, and crystallography. Graphic abstract: Monitoring the success of Cu(II)NTA labeling.
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Affiliation(s)
- Kevin Singewald
- Department of Chemistry, University of Pittsburgh, Pittsburgh, USA
| | | | - And Sunil Saxena
- Department of Chemistry, University of Pittsburgh, Pittsburgh, USA
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16
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Naydenova K, Muir KW, Wu LF, Zhang Z, Coscia F, Peet MJ, Castro-Hartmann P, Qian P, Sader K, Dent K, Kimanius D, Sutherland JD, Löwe J, Barford D, Russo CJ. Structure of the SARS-CoV-2 RNA-dependent RNA polymerase in the presence of favipiravir-RTP. Proc Natl Acad Sci U S A 2021; 118:e2021946118. [PMID: 33526596 PMCID: PMC7896311 DOI: 10.1073/pnas.2021946118] [Citation(s) in RCA: 121] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
The RNA polymerase inhibitor favipiravir is currently in clinical trials as a treatment for infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), despite limited information about the molecular basis for its activity. Here we report the structure of favipiravir ribonucleoside triphosphate (favipiravir-RTP) in complex with the SARS-CoV-2 RNA-dependent RNA polymerase (RdRp) bound to a template:primer RNA duplex, determined by electron cryomicroscopy (cryoEM) to a resolution of 2.5 Å. The structure shows clear evidence for the inhibitor at the catalytic site of the enzyme, and resolves the conformation of key side chains and ions surrounding the binding pocket. Polymerase activity assays indicate that the inhibitor is weakly incorporated into the RNA primer strand, and suppresses RNA replication in the presence of natural nucleotides. The structure reveals an unusual, nonproductive binding mode of favipiravir-RTP at the catalytic site of SARS-CoV-2 RdRp, which explains its low rate of incorporation into the RNA primer strand. Together, these findings inform current and future efforts to develop polymerase inhibitors for SARS coronaviruses.
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Affiliation(s)
- Katerina Naydenova
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Kyle W Muir
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Long-Fei Wu
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Ziguo Zhang
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Francesca Coscia
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Mathew J Peet
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Pablo Castro-Hartmann
- Materials and Structural Analysis, Thermo Fisher Scientific, 5651 GG Eindhoven, The Netherlands
| | - Pu Qian
- Materials and Structural Analysis, Thermo Fisher Scientific, 5651 GG Eindhoven, The Netherlands
| | - Kasim Sader
- Materials and Structural Analysis, Thermo Fisher Scientific, 5651 GG Eindhoven, The Netherlands
| | - Kyle Dent
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Dari Kimanius
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - John D Sutherland
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - David Barford
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
| | - Christopher J Russo
- Medical Research Council Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom;
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17
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Gardiner AT, Naydenova K, Castro-Hartmann P, Nguyen-Phan TC, Russo CJ, Sader K, Hunter CN, Cogdell RJ, Qian P. The 2.4 Å cryo-EM structure of a heptameric light-harvesting 2 complex reveals two carotenoid energy transfer pathways. SCIENCE ADVANCES 2021; 7:7/7/eabe4650. [PMID: 33579696 PMCID: PMC7880592 DOI: 10.1126/sciadv.abe4650] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 12/23/2020] [Indexed: 06/12/2023]
Abstract
We report the 2.4 Ångström resolution structure of the light-harvesting 2 (LH2) complex from Marichromatium (Mch.) purpuratum determined by cryogenic electron microscopy. The structure contains a heptameric ring that is unique among all known LH2 structures, explaining the unusual spectroscopic properties of this bacterial antenna complex. We identify two sets of distinct carotenoids in the structure and describe a network of energy transfer pathways from the carotenoids to bacteriochlorophyll a molecules. The geometry imposed by the heptameric ring controls the resonant coupling of the long-wavelength energy absorption band. Together, these details reveal key aspects of the assembly and oligomeric form of purple bacterial LH2 complexes that were previously inaccessible by any technique.
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Affiliation(s)
- Alastair T Gardiner
- Institute of Molecular, Cell and Systems Biology, Glasgow University, Glasgow G12 8QQ, UK
| | - Katerina Naydenova
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Pablo Castro-Hartmann
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - Tu C Nguyen-Phan
- Institute of Molecular, Cell and Systems Biology, Glasgow University, Glasgow G12 8QQ, UK
| | - Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Kasim Sader
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands
| | - C Neil Hunter
- Department of Molecular Biology, The University of Sheffield, Sheffield S10 2TN, UK
| | - Richard J Cogdell
- Institute of Molecular, Cell and Systems Biology, Glasgow University, Glasgow G12 8QQ, UK
| | - Pu Qian
- Materials and Structural Analysis, Thermo Fisher Scientific, Achtseweg Noord 5, 5651 GG Eindhoven, Netherlands.
- Department of Molecular Biology, The University of Sheffield, Sheffield S10 2TN, UK
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18
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Brito Querido J, Sokabe M, Kraatz S, Gordiyenko Y, Skehel JM, Fraser CS, Ramakrishnan V. Structure of a human 48 S translational initiation complex. Science 2020; 369:1220-1227. [PMID: 32883864 DOI: 10.1126/science.aba4904] [Citation(s) in RCA: 110] [Impact Index Per Article: 27.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Accepted: 07/07/2020] [Indexed: 12/20/2022]
Abstract
A key step in translational initiation is the recruitment of the 43S preinitiation complex by the cap-binding complex [eukaryotic initiation factor 4F (eIF4F)] at the 5' end of messenger RNA (mRNA) to form the 48S initiation complex (i.e., the 48S). The 48S then scans along the mRNA to locate a start codon. To understand the mechanisms involved, we used cryo-electron microscopy to determine the structure of a reconstituted human 48S The structure reveals insights into early events of translation initiation complex assembly, as well as how eIF4F interacts with subunits of eIF3 near the mRNA exit channel in the 43S The location of eIF4F is consistent with a slotting model of mRNA recruitment and suggests that downstream mRNA is unwound at least in part by being "pulled" through the 40S subunit during scanning.
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Affiliation(s)
| | - Masaaki Sokabe
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA
| | | | | | | | - Christopher S Fraser
- Department of Molecular and Cellular Biology, College of Biological Sciences, University of California, Davis, CA, USA.
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19
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Naydenova K, Jia P, Russo CJ. Cryo-EM with sub-1 Å specimen movement. Science 2020; 370:223-226. [PMID: 33033219 PMCID: PMC7116250 DOI: 10.1126/science.abb7927] [Citation(s) in RCA: 74] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/15/2020] [Indexed: 12/26/2022]
Abstract
Most information loss in cryogenic electron microscopy (cryo-EM) stems from particle movement during imaging, which remains poorly understood. We show that this movement is caused by buckling and subsequent deformation of the suspended ice, with a threshold that depends directly on the shape of the frozen water layer set by the support foil. We describe a specimen support design that eliminates buckling and reduces electron beam-induced particle movement to less than 1 angstrom. The design allows precise foil tracking during imaging with high-speed detectors, thereby lessening demands on cryostage precision and stability. It includes a maximal density of holes, which increases throughput in automated cryo-EM without degrading data quality. Movement-free imaging allows extrapolation to a three-dimensional map of the specimen at zero electron exposure, before the onset of radiation damage.
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Affiliation(s)
| | - Peipei Jia
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, UK
- ARC Centre of Excellence for Nanoscale BioPhotonics (CNBP), Institute for Photonics and Advanced Sensing, School of Physical Sciences, University of Adelaide, Adelaide 5005, Australia
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20
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Collier JE, Lee BG, Roig MB, Yatskevich S, Petela NJ, Metson J, Voulgaris M, Gonzalez Llamazares A, Löwe J, Nasmyth KA. Transport of DNA within cohesin involves clamping on top of engaged heads by Scc2 and entrapment within the ring by Scc3. eLife 2020; 9:e59560. [PMID: 32930661 PMCID: PMC7492086 DOI: 10.7554/elife.59560] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 08/30/2020] [Indexed: 12/13/2022] Open
Abstract
In addition to extruding DNA loops, cohesin entraps within its SMC-kleisin ring (S-K) individual DNAs during G1 and sister DNAs during S-phase. All three activities require related hook-shaped proteins called Scc2 and Scc3. Using thiol-specific crosslinking we provide rigorous proof of entrapment activity in vitro. Scc2 alone promotes entrapment of DNAs in the E-S and E-K compartments, between ATP-bound engaged heads and the SMC hinge and associated kleisin, respectively. This does not require ATP hydrolysis nor is it accompanied by entrapment within S-K rings, which is a slower process requiring Scc3. Cryo-EM reveals that DNAs transported into E-S/E-K compartments are 'clamped' in a sub-compartment created by Scc2's association with engaged heads whose coiled coils are folded around their elbow. We suggest that clamping may be a recurrent feature of cohesin complexes active in loop extrusion and that this conformation precedes the S-K entrapment required for sister chromatid cohesion.
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Affiliation(s)
- James E Collier
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Byung-Gil Lee
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | | | | | - Naomi J Petela
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | - Jean Metson
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
| | | | | | - Jan Löwe
- MRC Laboratory of Molecular BiologyCambridgeUnited Kingdom
| | - Kim A Nasmyth
- Department of Biochemistry, University of OxfordOxfordUnited Kingdom
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21
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Lee BG, Merkel F, Allegretti M, Hassler M, Cawood C, Lecomte L, O'Reilly FJ, Sinn LR, Gutierrez-Escribano P, Kschonsak M, Bravo S, Nakane T, Rappsilber J, Aragon L, Beck M, Löwe J, Haering CH. Cryo-EM structures of holo condensin reveal a subunit flip-flop mechanism. Nat Struct Mol Biol 2020; 27:743-751. [PMID: 32661420 DOI: 10.1038/s41594-020-0457-x] [Citation(s) in RCA: 61] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 05/28/2020] [Indexed: 01/01/2023]
Abstract
Complexes containing a pair of structural maintenance of chromosomes (SMC) family proteins are fundamental for the three-dimensional (3D) organization of genomes in all domains of life. The eukaryotic SMC complexes cohesin and condensin are thought to fold interphase and mitotic chromosomes, respectively, into large loop domains, although the underlying molecular mechanisms have remained unknown. We used cryo-EM to investigate the nucleotide-driven reaction cycle of condensin from the budding yeast Saccharomyces cerevisiae. Our structures of the five-subunit condensin holo complex at different functional stages suggest that ATP binding induces the transition of the SMC coiled coils from a folded-rod conformation into a more open architecture. ATP binding simultaneously triggers the exchange of the two HEAT-repeat subunits bound to the SMC ATPase head domains. We propose that these steps result in the interconversion of DNA-binding sites in the catalytic core of condensin, forming the basis of the DNA translocation and loop-extrusion activities.
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Affiliation(s)
| | - Fabian Merkel
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Matteo Allegretti
- Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Markus Hassler
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | | | - Léa Lecomte
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Collaboration for joint PhD degree between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Francis J O'Reilly
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | - Ludwig R Sinn
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany
| | | | - Marc Kschonsak
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.,Structural Biology, Genentech, South San Francisco, CA, USA
| | - Sol Bravo
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | | | - Juri Rappsilber
- Institute of Biotechnology, Technische Universität Berlin, Berlin, Germany.,Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Luis Aragon
- MRC London Institute of Medical Sciences, London, UK.
| | - Martin Beck
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Max Planck Institute of Biophysics, Frankfurt am Main, Germany.
| | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, UK.
| | - Christian H Haering
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany. .,Biocenter, Julius-Maximilians-Universität Würzburg, Würzburg, Germany.
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22
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Hoffmann PC, Bharat TAM, Wozny MR, Boulanger J, Miller EA, Kukulski W. Tricalbins Contribute to Cellular Lipid Flux and Form Curved ER-PM Contacts that Are Bridged by Rod-Shaped Structures. Dev Cell 2019; 51:488-502.e8. [PMID: 31743663 PMCID: PMC6863393 DOI: 10.1016/j.devcel.2019.09.019] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2019] [Revised: 08/06/2019] [Accepted: 09/25/2019] [Indexed: 11/25/2022]
Abstract
Lipid flow between cellular organelles occurs via membrane contact sites. Extended-synaptotagmins, known as tricalbins in yeast, mediate lipid transfer between the endoplasmic reticulum (ER) and plasma membrane (PM). How these proteins regulate membrane architecture to transport lipids across the aqueous space between bilayers remains unknown. Using correlative microscopy, electron cryo-tomography, and high-throughput genetics, we address the interplay of architecture and function in budding yeast. We find that ER-PM contacts differ in protein composition and membrane morphology, not in intermembrane distance. In situ electron cryo-tomography reveals the molecular organization of tricalbin-mediated contacts, suggesting a structural framework for putative lipid transfer. Genetic analysis uncovers functional overlap with cellular lipid routes, such as maintenance of PM asymmetry. Further redundancies are suggested for individual tricalbin protein domains. We propose a modularity of molecular and structural functions of tricalbins and of their roles within the cellular network of lipid distribution pathways.
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Affiliation(s)
- Patrick C Hoffmann
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, South Parks Road, Oxford OX1 3RE, UK; Central Oxford Structural Microscopy and Imaging Centre, South Parks Road, Oxford OX1 3RE, UK
| | - Michael R Wozny
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jerome Boulanger
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Elizabeth A Miller
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Wanda Kukulski
- Cell Biology Division, MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK.
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23
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Naydenova K, McMullan G, Peet MJ, Lee Y, Edwards PC, Chen S, Leahy E, Scotcher S, Henderson R, Russo CJ. CryoEM at 100 keV: a demonstration and prospects. IUCRJ 2019; 6:1086-1098. [PMID: 31709064 PMCID: PMC6830209 DOI: 10.1107/s2052252519012612] [Citation(s) in RCA: 68] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/10/2019] [Indexed: 05/23/2023]
Abstract
100 kV is investigated as the operating voltage for single-particle electron cryomicroscopy (cryoEM). Reducing the electron energy from the current standard of 300 or 200 keV offers both cost savings and potentially improved imaging. The latter follows from recent measurements of radiation damage to biological specimens by high-energy electrons, which show that at lower energies there is an increased amount of information available per unit damage. For frozen hydrated specimens around 300 Å in thickness, the predicted optimal electron energy for imaging is 100 keV. Currently available electron cryomicroscopes in the 100-120 keV range are not optimized for cryoEM as they lack both the spatially coherent illumination needed for the high defocus used in cryoEM and imaging detectors optimized for 100 keV electrons. To demonstrate the potential of imaging at 100 kV, the voltage of a standard, commercial 200 kV field-emission gun (FEG) microscope was reduced to 100 kV and a side-entry cryoholder was used. As high-efficiency, large-area cameras are not currently available for 100 keV electrons, a commercial hybrid pixel camera designed for X-ray detection was attached to the camera chamber and was used for low-dose data collection. Using this configuration, five single-particle specimens were imaged: hepatitis B virus capsid, bacterial 70S ribosome, catalase, DNA protection during starvation protein and haemoglobin, ranging in size from 4.5 MDa to 64 kDa with corresponding diameters from 320 to 72 Å. These five data sets were used to reconstruct 3D structures with resolutions between 8.4 and 3.4 Å. Based on this work, the practical advantages and current technological limitations to single-particle cryoEM at 100 keV are considered. These results are also discussed in the context of future microscope development towards the goal of rapid, simple and widely available structure determination of any purified biological specimen.
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Affiliation(s)
- K. Naydenova
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - G. McMullan
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - M. J. Peet
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - Y. Lee
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - P. C. Edwards
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - S. Chen
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - E. Leahy
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - S. Scotcher
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - R. Henderson
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
| | - C. J. Russo
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, England
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24
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Abstract
Single-particle electron cryomicroscopy (cryoEM) has now proved to be the method of choice for determining the structure of biological macromolecules and complexes. Yet success in determining a structure by cryoEM depends on being able to prepare a frozen specimen on a small metal support called a grid. This process is poorly controlled at present because of molecule–surface interactions. Here we used a modified form of graphene, in conjunction with a stable grid made of gold, to control these surface effects. Functionalized graphene-on-gold grids improve the reliability of specimen preparation and enhance image quality. This technology has the potential to take specimen preparation for cryoEM from a trial and error art to a controlled and reproducible process. With recent technological advances, the atomic resolution structure of any purified biomolecular complex can, in principle, be determined by single-particle electron cryomicroscopy (cryoEM). In practice, the primary barrier to structure determination is the preparation of a frozen specimen suitable for high-resolution imaging. To address this, we present a multifunctional specimen support for cryoEM, comprising large-crystal monolayer graphene suspended across the surface of an ultrastable gold specimen support. Using a low-energy plasma surface modification system, we tune the surface of this support to the specimen by patterning a range of covalent functionalizations across the graphene layer on a single grid. This support design reduces specimen movement during imaging, improves image quality, and allows high-resolution structure determination with a minimum of material and data.
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Russo CJ, Henderson R. Charge accumulation in electron cryomicroscopy. Ultramicroscopy 2018; 187:43-49. [PMID: 29413411 PMCID: PMC5862658 DOI: 10.1016/j.ultramic.2018.01.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/09/2018] [Accepted: 01/17/2018] [Indexed: 11/17/2022]
Abstract
A physical account of charge accumulation in low-dose cryoEM is presented. We describe electrostatic micro-lenses that are extremely sensitive charge detectors. These micro-lenses allow the direct measurement of charge accumulation. Charge build-up saturates within the first millisecond of a typical micrograph.
When irradiated in a transmission electron microscope, plunge-frozen, amorphous water ice specimens accumulate a pattern of static charge that changes dynamically as the specimen is irradiated, and which can deflect the transmitted electrons and blur the resultant micrographs. Here we provide a physical description of this charge accumulation and characterise its dynamic behaviour in the context of low-dose electron cryomicroscopy (cryoEM). We observe the accumulation of positive charge in the primary irradiation area as expected from earlier work. To our surprise, we also observed a build-up of negative charge in nearby unirradiated regions of the specimen. Using a standard carbon support foil containing a pure water ice specimen, we collect a portion of this negative charge in the micrometer sized specimen holes which act as electrostatic lenses. These unusual, diverging micro-lenses are extremely sensitive charge detectors that allow us to directly measure the magnitude and dynamics of charge accumulation and neutralisation that occur during cryoEM imaging. Using these measurements, we find that the build-up of charge on the specimen saturates to a dynamic equilibrium at an electron fluence which is orders of magnitude lower than required for a typical low-dose micrograph. The measurements here will guide the development of optimal imaging conditions for biological specimens and contribute to a complete theory of information loss in electron cryomicroscopy.
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Affiliation(s)
- Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH UK.
| | - Richard Henderson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH UK
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Russo CJ, Henderson R. Microscopic charge fluctuations cause minimal contrast loss in cryoEM. Ultramicroscopy 2018; 187:56-63. [PMID: 29413413 PMCID: PMC5862660 DOI: 10.1016/j.ultramic.2018.01.011] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/09/2018] [Accepted: 01/17/2018] [Indexed: 11/26/2022]
Abstract
A physical account of charge fluctuations in low-dose cryoEM is presented. We quantify the bee swarm charging phenomenon on cryoEM specimen. We measure the envelope function caused by charge fluctuations. The effects of these fluctuations are negligible in cryoEM.
The fluctuating granularity or “bee swarm” effect seen in highly defocussed transmission electron micrographs is caused by microscopic charge fluctuations in the specimen created by the illuminating beam. In the field of high-resolution single particle electron cryomicroscopy (cryoEM), there has been a concern that this fluctuating charge might cause defocus-dependent Thon ring fading which would degrade the final image. In this paper, we have analysed the 2.35 Å fringes from the (111) reflection in images of gold nanoparticles embedded in amorphous ice. We show that there is a small, yet detectable amount of defocus-dependent blurring of the lattice fringes when compared with those from a pure gold foil. The transverse electric field associated with the fluctuating charges on the insulating frozen water specimen deflects the electron beam locally and causes image blurring. The perturbation is small, decreasing the amplitude of the 2.35 Å reflection at 10 µm defocus by about 7% (intensity by 14%). For smaller defocus values in the range 2–4 µm and for resolutions that are typical in cryoEM, the effects of source incoherence and the bee swarm effect are negligible for all reasonable cryoEM imaging conditions, assuming that a field emission gun (FEG) is used for illumination. This leaves physical movement of the specimen due to radiation damage as the outstanding problem and the major source of contrast loss in cryoEM micrographs.
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Affiliation(s)
- Christopher J Russo
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH UK.
| | - Richard Henderson
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH UK
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Wagstaff JM, Tsim M, Oliva MA, García-Sanchez A, Kureisaite-Ciziene D, Andreu JM, Löwe J. A Polymerization-Associated Structural Switch in FtsZ That Enables Treadmilling of Model Filaments. mBio 2017; 8:e00254-17. [PMID: 28465423 PMCID: PMC5414002 DOI: 10.1128/mbio.00254-17] [Citation(s) in RCA: 67] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Accepted: 04/13/2017] [Indexed: 02/07/2023] Open
Abstract
Bacterial cell division in many organisms involves a constricting cytokinetic ring that is orchestrated by the tubulin-like protein FtsZ. FtsZ forms dynamic filaments close to the membrane at the site of division that have recently been shown to treadmill around the division ring, guiding septal wall synthesis. Here, using X-ray crystallography of Staphylococcus aureus FtsZ (SaFtsZ), we reveal how an FtsZ can adopt two functionally distinct conformations, open and closed. The open form is found in SaFtsZ filaments formed in crystals and also in soluble filaments of Escherichia coli FtsZ as deduced by electron cryomicroscopy. The closed form is found within several crystal forms of two nonpolymerizing SaFtsZ mutants and corresponds to many previous FtsZ structures from other organisms. We argue that FtsZ's conformational switch is polymerization-associated, driven by the formation of the longitudinal intersubunit interfaces along the filament. We show that such a switch provides explanations for both how treadmilling may occur within a single-stranded filament and why filament assembly is cooperative.IMPORTANCE The FtsZ protein is a key molecule during bacterial cell division. FtsZ forms filaments that organize cell membrane constriction, as well as remodeling of the cell wall, to divide cells. FtsZ functions through nucleotide-driven filament dynamics that are poorly understood at the molecular level. In particular, mechanisms for cooperative assembly (nonlinear dependency on concentration) and treadmilling (preferential growth at one filament end and loss at the other) have remained elusive. Here, we show that most likely all FtsZ proteins have two distinct conformations, a "closed" form in monomeric FtsZ and an "open" form in filaments. The conformational switch that occurs upon polymerization explains cooperativity and, in concert with polymerization-dependent nucleotide hydrolysis, efficient treadmilling of FtsZ polymers.
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Affiliation(s)
| | - Matthew Tsim
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
| | - María A Oliva
- Centro de Investigaciones Biológicas, CSIC, Madrid, Spain
| | | | | | | | - Jan Löwe
- MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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