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Chua EYD, Alink LM, Kopylov M, Johnston JD, Eisenstein F, de Marco A. Square beams for optimal tiling in transmission electron microscopy. Nat Methods 2024; 21:562-565. [PMID: 38238558 PMCID: PMC11009100 DOI: 10.1038/s41592-023-02161-x] [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] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024]
Abstract
Imaging large fields of view at a high magnification requires tiling. Transmission electron microscopes typically have round beam profiles; therefore, tiling across a large area is either imperfect or results in uneven exposures, a problem for dose-sensitive samples. Here, we introduce a square electron beam that can easily be retrofitted in existing microscopes, and demonstrate its application, showing that it can tile nearly perfectly and deliver cryo-electron microscopy imaging with a resolution comparable to conventional set-ups.
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Affiliation(s)
- Eugene Y D Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Lambertus M Alink
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
| | - Jake D Johnston
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | | | - Alex de Marco
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY, USA.
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA.
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2
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Abstract
Imaging large fields of view at a high magnification requires tiling. Transmission electron microscopes typically have round beam profiles; therefore, tiling across a large area is either imperfect or results in uneven exposures, a problem on dose-sensitive samples. Here, we introduce a square electron beam that can be easily retrofitted in existing microscopes and demonstrate its application, showing it can tile nearly perfectly and deliver cryo-EM imaging with a resolution comparable to conventional setups.
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Affiliation(s)
- Eugene YD Chua
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027
| | - Lambertus M Alink
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027
| | - Mykhailo Kopylov
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027
| | - Jake Johnston
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027
- Department of Physiology and Cellular Biophysics, Columbia University, New York, NY, USA
| | | | - Alex de Marco
- Simons Electron Microscopy Center, New York Structural Biology Center, New York, NY 10027
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3
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Eisenstein F, Yanagisawa H, Kashihara H, Kikkawa M, Tsukita S, Danev R. Parallel cryo electron tomography on in situ lamellae. Nat Methods 2023; 20:131-138. [PMID: 36456783 DOI: 10.1038/s41592-022-01690-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 32.0] [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: 03/22/2022] [Accepted: 09/28/2022] [Indexed: 12/05/2022]
Abstract
In situ cryo electron tomography of cryo focused ion beam milled samples has emerged in recent years as a powerful technique for structural studies of macromolecular complexes in their native cellular environment. However, the possibilities for recording tomographic tilt series in a high-throughput manner are limited, in part by the lamella-shaped samples. Here we utilize a geometrical sample model and optical image shift to record tens of tilt series in parallel, thereby saving time and gaining access to sample areas conventionally used for tracking specimen movement. The parallel cryo electron tomography (PACE-tomo) method achieves a throughput faster than 5 min per tilt series and allows for the collection of sample areas that were previously unreachable, thus maximizing the amount of data from each lamella. Performance testing with ribosomes in vitro and in situ on state-of-the-art and general-purpose microscopes demonstrated the high throughput and quality of PACE-tomo.
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Affiliation(s)
| | | | - Hiroka Kashihara
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
| | | | - Sachiko Tsukita
- Advanced Comprehensive Research Organization, Teikyo University, Tokyo, Japan
| | - Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan.
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4
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Xu J, Ericson CF, Lien YW, Rutaganira FUN, Eisenstein F, Feldmüller M, King N, Pilhofer M. Publisher Correction: Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis. Nat Microbiol 2022; 7:737. [PMID: 35379983 PMCID: PMC9064796 DOI: 10.1038/s41564-022-01111-1] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Affiliation(s)
- Jingwei Xu
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, Zürich, Switzerland
| | - Charles F Ericson
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, Zürich, Switzerland
| | - Yun-Wei Lien
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, Zürich, Switzerland
| | - Florentine U N Rutaganira
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Fabian Eisenstein
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, Zürich, Switzerland.,Graduate School of Medicine, University of Tokyo, N415, 7-3-1 Hongo, Bunkyo-ku, Tokyo, Japan
| | - Miki Feldmüller
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, Zürich, Switzerland
| | - Nicole King
- Howard Hughes Medical Institute and Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology & Biophysics, Eidgenössische Technische Hochschule Zürich, Otto-Stern-Weg 5, Zürich, Switzerland.
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5
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Xu J, Ericson CF, Lien YW, Rutaganira FUN, Eisenstein F, Feldmüller M, King N, Pilhofer M. Identification and structure of an extracellular contractile injection system from the marine bacterium Algoriphagus machipongonensis. Nat Microbiol 2022; 7:397-410. [PMID: 35165385 PMCID: PMC8894135 DOI: 10.1038/s41564-022-01059-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 01/05/2022] [Indexed: 12/11/2022]
Abstract
Contractile injection systems (CISs) are phage tail-like nanomachines, mediating bacterial cell–cell interactions as either type VI secretion systems (T6SSs) or extracellular CISs (eCISs). Bioinformatic studies uncovered a phylogenetic group of hundreds of putative CIS gene clusters that are highly diverse and widespread; however, only four systems have been characterized. Here we studied a putative CIS gene cluster in the marine bacterium Algoriphagus machipongonensis. Using an integrative approach, we show that the system is compatible with an eCIS mode of action. Our cryo-electron microscopy structure revealed several features that differ from those seen in other CISs: a ‘cap adaptor’ located at the distal end, a ‘plug’ exposed to the tube lumen, and a ‘cage’ formed by massive extensions of the baseplate. These elements are conserved in other CISs, and our genetic tools identified that they are required for assembly, cargo loading and function. Furthermore, our atomic model highlights specific evolutionary hotspots and will serve as a framework for understanding and re−engineering CISs. The characterization of an extracellular contractile injection system (eCIS) from the marine bacterium Algoriphagus machipongonensis (AlgoCIS) reveals structural features linked to the assembly and function of this nanomachine.
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Danev R, Belousoff M, Liang YL, Zhang X, Eisenstein F, Wootten D, Sexton PM. Routine sub-2.5 Å cryo-EM structure determination of GPCRs. Nat Commun 2021; 12:4333. [PMID: 34267200 PMCID: PMC8282782 DOI: 10.1038/s41467-021-24650-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 01/25/2021] [Accepted: 06/29/2021] [Indexed: 11/24/2022] Open
Abstract
Cryo-electron microscopy (cryo-EM) of small membrane proteins, such as G protein-coupled receptors (GPCRs), remains challenging. Pushing the performance boundaries of the technique requires quantitative knowledge about the contribution of multiple factors. Here, we present an in-depth analysis and optimization of the main experimental parameters in cryo-EM. We combined actual structural studies with methods development to quantify the effects of the Volta phase plate, zero-loss energy filtering, objective lens aperture, defocus magnitude, total exposure, and grid type. By using this information to carefully maximize the experimental performance, it is now possible to routinely determine GPCR structures at resolutions better than 2.5 Å. The improved fidelity of such maps enables the building of better atomic models and will be crucial for the future expansion of cryo-EM into the structure-based drug design domain. The optimization guidelines given here are not limited to GPCRs and can be applied directly to other small proteins.
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Affiliation(s)
- Radostin Danev
- Graduate School of Medicine, University of Tokyo, Tokyo, Japan.
| | - Matthew Belousoff
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Yi-Lynn Liang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- Confo Therapeutics, Ghent (Zwijnaarde), Belgium
| | - Xin Zhang
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | | | - Denise Wootten
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
| | - Patrick M Sexton
- Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
- ARC Centre for Cryo-electron Microscopy of Membrane Proteins, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC, Australia
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Rocchi I, Ericson CF, Malter KE, Zargar S, Eisenstein F, Pilhofer M, Beyhan S, Shikuma NJ. A Bacterial Phage Tail-like Structure Kills Eukaryotic Cells by Injecting a Nuclease Effector. Cell Rep 2020; 28:295-301.e4. [PMID: 31291567 DOI: 10.1016/j.celrep.2019.06.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [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: 02/12/2019] [Revised: 05/09/2019] [Accepted: 06/05/2019] [Indexed: 11/28/2022] Open
Abstract
Many bacteria interact with target organisms using syringe-like structures called contractile injection systems (CISs). CISs structurally resemble headless bacteriophages and share evolutionarily related proteins such as the tail tube, sheath, and baseplate complex. In many cases, CISs mediate trans-kingdom interactions between bacteria and eukaryotes by delivering effectors to target cells. However, the specific effectors and their modes of action are often unknown. Here, we establish an ex vivo model to study an extracellular CIS (eCIS) called metamorphosis-associated contractile structures (MACs) that target eukaryotic cells. MACs kill two eukaryotic cell lines, fall armyworm Sf9 cells and J774A.1 murine macrophage cells, by translocating an effector termed Pne1. Before the identification of Pne1, no CIS effector exhibiting nuclease activity against eukaryotic cells had been described. Our results define a new mechanism of CIS-mediated bacteria-eukaryote interaction and are a step toward developing CISs as novel delivery systems for eukaryotic hosts.
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Affiliation(s)
- Iara Rocchi
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Charles F Ericson
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Kyle E Malter
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA
| | - Sahar Zargar
- Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Fabian Eisenstein
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, Department of Biology, ETH Zürich, Otto-Stern-Weg 5, 8093 Zürich, Switzerland
| | - Sinem Beyhan
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA.
| | - Nicholas J Shikuma
- Department of Biology, San Diego State University, San Diego, CA 92182, USA; Viral Information Institute, San Diego State University, San Diego, CA 92182, USA; Department of Infectious Diseases, J. Craig Venter Institute, La Jolla, CA 92037, USA.
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Ericson CF, Eisenstein F, Medeiros JM, Malter KE, Cavalcanti GS, Zeller RW, Newman DK, Pilhofer M, Shikuma NJ. A contractile injection system stimulates tubeworm metamorphosis by translocating a proteinaceous effector. eLife 2019; 8:46845. [PMID: 31526475 PMCID: PMC6748791 DOI: 10.7554/elife.46845] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [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: 03/14/2019] [Accepted: 08/05/2019] [Indexed: 12/25/2022] Open
Abstract
The swimming larvae of many marine animals identify a location on the sea floor to undergo metamorphosis based on the presence of specific bacteria. Although this microbe–animal interaction is critical for the life cycles of diverse marine animals, what types of biochemical cues from bacteria that induce metamorphosis has been a mystery. Metamorphosis of larvae of the tubeworm Hydroides elegans is induced by arrays of phage tail-like contractile injection systems, which are released by the bacterium Pseudoalteromonas luteoviolacea. Here we identify the novel effector protein Mif1. By cryo-electron tomography imaging and functional assays, we observe Mif1 as cargo inside the tube lumen of the contractile injection system and show that the mif1 gene is required for inducing metamorphosis. Purified Mif1 is sufficient for triggering metamorphosis when electroporated into tubeworm larvae. Our results indicate that the delivery of protein effectors by contractile injection systems may orchestrate microbe–animal interactions in diverse contexts. Many marine animals, including corals and tubeworms, begin life as larvae swimming in open water before transforming into adults that anchor themselves to the seabed. These transformations, known as metamorphoses, are often triggered by certain types of bacteria that form friendly relationships (or “symbioses”) with the animals. One such symbiosis forms between a bacterium called Pseudoalteromonas luteoviolacea and a tubeworm known as Hydroides elegans. Previous studies have shown that P. luteoviolacea produces syringe-like structures known as Metamorphosis Associated Contractile structures (or MACs for short) that are responsible for stimulating metamorphosis in the tubeworm larvae. Some viruses that infect bacteria use similar structures to inject molecules into their host cells. However, it was not clear whether MACs were also able to inject molecules into cells. Here, Ericson, Eisenstein et al. used a technique called cryo-electron tomography combined with genetic and biochemical approaches to study how the MACs of P. luteoviolacea trigger metamorphosis in tubeworms. The experiments identified a protein in the bacteria named Mif1 that was required for the tubeworms to transform. The bacteria loaded Mif1 into the tube of the MAC structure and then injected it into the tubeworms. Further experiments showed that inserting Mif1 alone into tubeworms was sufficient to activate metamorphosis. Mif1 is the first protein from bacteria to be shown to activate metamorphosis, but it is likely that many more remain to be discovered. Since other marine animals also form symbioses with bacteria, understanding how Mif1 and other similar proteins work may inform efforts to restore coral reefs and other fragile ecosystems, and increase the production of oysters and other shellfish. Furthermore, MACs and related structures may have the potential to be developed into biotechnology tools that deliver drugs and other molecules directly into animal cells.
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Affiliation(s)
- Charles F Ericson
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States.,Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Fabian Eisenstein
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - João M Medeiros
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Kyle E Malter
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Giselle S Cavalcanti
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
| | - Robert W Zeller
- Department of Biology, San Diego State University, San Diego, United States
| | - Dianne K Newman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Division of Geological and Planetary Sciences, California Institute of Technology, Pasadena, United States
| | - Martin Pilhofer
- Department of Biology, Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule, Zürich, Switzerland
| | - Nicholas J Shikuma
- Department of Biology, San Diego State University, San Diego, United States.,Viral Information Institute, San Diego State University, San Diego, United States
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9
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Eisenstein F. A health service program for children in day care. Children 1966; 13:237-40. [PMID: 5980808] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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