1
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Kaplan M, Chang YW, Oikonomou CM, Nicolas WJ, Jewett AI, Kreida S, Dutka P, Rettberg LA, Maggi S, Jensen GJ. Bdellovibrio predation cycle characterized at nanometre-scale resolution with cryo-electron tomography. Nat Microbiol 2023; 8:1267-1279. [PMID: 37349588 PMCID: PMC11061892 DOI: 10.1038/s41564-023-01401-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 04/27/2023] [Indexed: 06/24/2023]
Abstract
Bdellovibrio bacteriovorus is a microbial predator that offers promise as a living antibiotic for its ability to kill Gram-negative bacteria, including human pathogens. Even after six decades of study, fundamental details of its predation cycle remain mysterious. Here we used cryo-electron tomography to comprehensively image the lifecycle of B. bacteriovorus at nanometre-scale resolution. With high-resolution images of predation in a native (hydrated, unstained) state, we discover several surprising features of the process, including macromolecular complexes involved in prey attachment/invasion and a flexible portal structure lining a hole in the prey peptidoglycan that tightly seals the prey outer membrane around the predator during entry. Unexpectedly, we find that B. bacteriovorus does not shed its flagellum during invasion, but rather resorbs it into its periplasm for degradation. Finally, following growth and division in the bdelloplast, we observe a transient and extensive ribosomal lattice on the condensed B. bacteriovorus nucleoid.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Microbiology, University of Chicago, Chicago, IL, USA.
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - William J Nicolas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrew I Jewett
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Stefan Kreida
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Solna, Sweden
| | - Przemysław Dutka
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA, USA
| | | | - Stefano Maggi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT, USA.
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2
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Kaplan M, Oikonomou CM, Wood CR, Chreifi G, Subramanian P, Ortega DR, Chang Y, Beeby M, Shaffer CL, Jensen GJ. Novel transient cytoplasmic rings stabilize assembling bacterial flagellar motors. EMBO J 2022; 41:e109523. [PMID: 35301732 PMCID: PMC9108667 DOI: 10.15252/embj.2021109523] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 08/22/2021] [Revised: 01/31/2022] [Accepted: 02/16/2022] [Indexed: 12/20/2022] Open
Abstract
The process by which bacterial cells build their intricate flagellar motility apparatuses has long fascinated scientists. Our understanding of this process comes mainly from studies of purified flagella from two species, Escherichia coli and Salmonella enterica. Here, we used electron cryo-tomography (cryo-ET) to image the assembly of the flagellar motor in situ in diverse Proteobacteria: Hylemonella gracilis, Helicobacter pylori, Campylobacter jejuni, Pseudomonas aeruginosa, Pseudomonas fluorescens, and Shewanella oneidensis. Our results reveal the in situ structures of flagellar intermediates, beginning with the earliest flagellar type III secretion system core complex (fT3SScc) and MS-ring. In high-torque motors of Beta-, Gamma-, and Epsilon-proteobacteria, we discovered novel cytoplasmic rings that interact with the cytoplasmic torque ring formed by FliG. These rings, associated with the MS-ring, assemble very early and persist until the stators are recruited into their periplasmic ring; in their absence the stator ring does not assemble. By imaging mutants in Helicobacter pylori, we found that the fT3SScc proteins FliO and FliQ are required for the assembly of these novel cytoplasmic rings. Our results show that rather than a simple accretion of components, flagellar motor assembly is a dynamic process in which accessory components interact transiently to assist in building the complex nanomachine.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Catherine M Oikonomou
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Cecily R Wood
- Department of Veterinary ScienceUniversity of KentuckyLexingtonKYUSA
| | - Georges Chreifi
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Poorna Subramanian
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Davi R Ortega
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Yi‐Wei Chang
- Department of Biochemistry and BiophysicsPerelman School of MedicineUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Morgan Beeby
- Department of Life SciencesImperial College LondonLondonUK
| | - Carrie L Shaffer
- Department of Veterinary ScienceUniversity of KentuckyLexingtonKYUSA
- Department of Microbiology, Immunology, and Molecular GeneticsUniversity of KentuckyLexingtonKYUSA
- Department of Pharmaceutical SciencesUniversity of KentuckyLexingtonKYUSA
| | - Grant J Jensen
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
- Department of Chemistry and BiochemistryBrigham Young UniversityProvoUTUSA
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3
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Kaplan M, Chreifi G, Metskas LA, Liedtke J, Wood CR, Oikonomou CM, Nicolas WJ, Subramanian P, Zacharoff LA, Wang Y, Chang YW, Beeby M, Dobro MJ, Zhu Y, McBride MJ, Briegel A, Shaffer CL, Jensen GJ. In situ imaging of bacterial outer membrane projections and associated protein complexes using electron cryo-tomography. eLife 2021; 10:73099. [PMID: 34468314 PMCID: PMC8455137 DOI: 10.7554/elife.73099] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 08/17/2021] [Accepted: 08/23/2021] [Indexed: 12/19/2022] Open
Abstract
The ability to produce outer membrane projections in the form of tubular membrane extensions (MEs) and membrane vesicles (MVs) is a widespread phenomenon among diderm bacteria. Despite this, our knowledge of the ultrastructure of these extensions and their associated protein complexes remains limited. Here, we surveyed the ultrastructure and formation of MEs and MVs, and their associated protein complexes, in tens of thousands of electron cryo-tomograms of ~90 bacterial species that we have collected for various projects over the past 15 years (Jensen lab database), in addition to data generated in the Briegel lab. We identified outer MEs and MVs in 13 diderm bacterial species and classified several major ultrastructures: (1) tubes with a uniform diameter (with or without an internal scaffold), (2) tubes with irregular diameter, (3) tubes with a vesicular dilation at their tip, (4) pearling tubes, (5) connected chains of vesicles (with or without neck-like connectors), (6) budding vesicles and nanopods. We also identified several protein complexes associated with these MEs and MVs which were distributed either randomly or exclusively at the tip. These complexes include a secretin-like structure and a novel crown-shaped structure observed primarily in vesicles from lysed cells. In total, this work helps to characterize the diversity of bacterial membrane projections and lays the groundwork for future research in this field.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Georges Chreifi
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Lauren Ann Metskas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Janine Liedtke
- Leiden University, Sylvius Laboratories, Leiden, Netherlands
| | - Cecily R Wood
- Department of Veterinary Science, University of Kentucky, Lexington, United States
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - William J Nicolas
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Poorna Subramanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Lori A Zacharoff
- Department of Physics and Astronomy, University of Southern California, Los Angeles, United States
| | - Yuhang Wang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Yi-Wei Chang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, United States
| | - Morgan Beeby
- Department of Life Sciences, Imperial College London, London, United Kingdom
| | | | - Yongtao Zhu
- Department of Biological Sciences, Minnesota State University, Mankato, United States
| | - Mark J McBride
- Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, United States
| | - Ariane Briegel
- Leiden University, Sylvius Laboratories, Leiden, Netherlands
| | - Carrie L Shaffer
- Department of Veterinary Science, University of Kentucky, Lexington, United States.,Department of Microbiology, Immunology, and Molecular Genetics, University of Kentucky, Lexington, United States.,Department of Pharmaceutical Sciences, University of Kentucky, Lexington, United States
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Department of Chemistry and Biochemistry, Brigham Young University, Provo, United States
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Oikonomou CM, Jensen GJ. The Atlas of Bacterial & Archaeal Cell Structure: an Interactive Open-Access Microbiology Textbook. J Microbiol Biol Educ 2021; 22:jmbe00128-21. [PMID: 34594449 PMCID: PMC8442016 DOI: 10.1128/jmbe.00128-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Accepted: 07/22/2021] [Indexed: 06/13/2023]
Abstract
Here, we describe a new open-access digital textbook for microbiology, The Atlas of Bacterial & Archaeal Cell Structure (available at cellstructureatlas.org). The book addresses a fundamental gap in existing textbooks, namely, what bacterial and archaeal cells look like and how the macromolecular structures they contain give rise to their diverse and complex functions. The interactive, multimedia resource features real data from more than 150 cells belonging to approximately 70 different species, imaged by cutting-edge cryogenic electron microscopy (cryo-EM). Complementary animations show the cellular machinery in action. Only a basic familiarity with fundamental biology concepts is required to understand the material, which targets a wide range of students in courses from general biology for nonmajors to specialized graduate-level microbiology. The content can be digested in several hours, making it well suited to be assigned as a supplemental resource for a course covering either more diverse topics in cell biology or a more specialized topic such as medical microbiology. By making this resource freely available online, we hope it will serve students in diverse educational settings, including self-directed learners.
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Affiliation(s)
- Catherine M. Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
| | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, USA
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah, USA
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Mageswaran SK, Yang WY, Chakrabarty Y, Oikonomou CM, Jensen GJ. A cryo-electron tomography workflow reveals protrusion-mediated shedding on injured plasma membrane. Sci Adv 2021; 7:7/13/eabc6345. [PMID: 33771860 PMCID: PMC7997517 DOI: 10.1126/sciadv.abc6345] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Accepted: 02/09/2021] [Indexed: 06/12/2023]
Abstract
Cryo-electron tomography (cryo-ET) provides structural context to molecular mechanisms underlying biological processes. Although straightforward to implement for studying stable macromolecular complexes, using it to locate short-lived structures and events can be impractical. A combination of live-cell microscopy, correlative light and electron microscopy, and cryo-ET will alleviate this issue. We developed a workflow combining the three to study the ubiquitous and dynamic process of shedding in response to plasma membrane damage in HeLa cells. We found filopodia-like protrusions enriched at damage sites and acting as scaffolds for shedding, which involves F-actin dynamics, myosin-1a, and vacuolar protein sorting 4B (a component of the 'endosomal sorting complex required for transport' machinery). Overall, shedding is more complex than current models of vesiculation from flat membranes. Its similarities to constitutive shedding in enterocytes argue for a conserved mechanism. Our workflow can also be adapted to study other damage response pathways and dynamic cellular events.
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Affiliation(s)
- Shrawan Kumar Mageswaran
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Biophysics and Biochemistry, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Wei Yuan Yang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan.
| | - Yogaditya Chakrabarty
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA.
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, UT 84604, USA
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Kaplan M, Subramanian P, Ghosal D, Oikonomou CM, Pirbadian S, Starwalt‐Lee R, Mageswaran SK, Ortega DR, Gralnick JA, El‐Naggar MY, Jensen GJ. In situ imaging of the bacterial flagellar motor disassembly and assembly processes. EMBO J 2019; 38:e100957. [PMID: 31304634 PMCID: PMC6627242 DOI: 10.15252/embj.2018100957] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [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: 10/18/2018] [Revised: 04/11/2019] [Accepted: 04/18/2019] [Indexed: 11/09/2022] Open
Abstract
The self-assembly of cellular macromolecular machines such as the bacterial flagellar motor requires the spatio-temporal synchronization of gene expression with proper protein localization and association of dozens of protein components. In Salmonella and Escherichia coli, a sequential, outward assembly mechanism has been proposed for the flagellar motor starting from the inner membrane, with the addition of each new component stabilizing the previous one. However, very little is known about flagellar disassembly. Here, using electron cryo-tomography and sub-tomogram averaging of intact Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis cells, we study flagellar motor disassembly and assembly in situ. We first show that motor disassembly results in stable outer membrane-embedded sub-complexes. These sub-complexes consist of the periplasmic embellished P- and L-rings, and bend the membrane inward while it remains apparently sealed. Additionally, we also observe various intermediates of the assembly process including an inner-membrane sub-complex consisting of the C-ring, MS-ring, and export apparatus. Finally, we show that the L-ring is responsible for reshaping the outer membrane, a crucial step in the flagellar assembly process.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Poorna Subramanian
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Debnath Ghosal
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Catherine M Oikonomou
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Sahand Pirbadian
- Department of Physics and Astronomy, Biological Sciences, and ChemistryUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Ruth Starwalt‐Lee
- BioTechnology InstituteUniversity of Minnesota – Twin CitiesSt. PaulMNUSA
| | | | - Davi R Ortega
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
| | - Jeffrey A Gralnick
- BioTechnology InstituteUniversity of Minnesota – Twin CitiesSt. PaulMNUSA
- Department of Plant and Microbial BiologyUniversity of Minnesota – Twin CitiesSt. PaulMNUSA
| | - Mohamed Y El‐Naggar
- Department of Physics and Astronomy, Biological Sciences, and ChemistryUniversity of Southern CaliforniaLos AngelesCAUSA
| | - Grant J Jensen
- Division of Biology and Biological EngineeringCalifornia Institute of TechnologyPasadenaCAUSA
- Howard Hughes Medical InstituteCalifornia Institute of TechnologyPasadenaCAUSA
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Ortega DR, Oikonomou CM, Ding HJ, Rees-Lee P, Jensen GJ. ETDB-Caltech: A blockchain-based distributed public database for electron tomography. PLoS One 2019; 14:e0215531. [PMID: 30986271 PMCID: PMC6464211 DOI: 10.1371/journal.pone.0215531] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 04/03/2019] [Indexed: 01/12/2023] Open
Abstract
Three-dimensional electron microscopy techniques like electron tomography provide valuable insights into cellular structures, and present significant challenges for data storage and dissemination. Here we explored a novel method to publicly release more than 11,000 such datasets, more than 30 TB in total, collected by our group. Our method, based on a peer-to-peer file sharing network built around a blockchain ledger, offers a distributed solution to data storage. In addition, we offer a user-friendly browser-based interface, https://etdb.caltech.edu, for anyone interested to explore and download our data. We discuss the relative advantages and disadvantages of this system and provide tools for other groups to mine our data and/or use the same approach to share their own imaging datasets.
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Affiliation(s)
- Davi R. Ortega
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Catherine M. Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - H. Jane Ding
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | - Prudence Rees-Lee
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
| | | | - Grant J. Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California, United States of America
- Howard Hughes Medical Institute, Pasadena, California, United States of America
- * E-mail:
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8
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Nguyen LT, Oikonomou CM, Ding HJ, Kaplan M, Yao Q, Chang YW, Beeby M, Jensen GJ. Simulations suggest a constrictive force is required for Gram-negative bacterial cell division. Nat Commun 2019; 10:1259. [PMID: 30890709 PMCID: PMC6425016 DOI: 10.1038/s41467-019-09264-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2018] [Accepted: 02/28/2019] [Indexed: 11/16/2022] Open
Abstract
To divide, Gram-negative bacterial cells must remodel cell wall at the division site. It remains debated, however, whether this cell wall remodeling alone can drive membrane constriction, or if a constrictive force from the tubulin homolog FtsZ is required. Previously, we constructed software (REMODELER 1) to simulate cell wall remodeling during growth. Here, we expanded this software to explore cell wall division (REMODELER 2). We found that simply organizing cell wall synthesis complexes at the midcell is not sufficient to cause invagination, even with the implementation of a make-before-break mechanism, in which new hoops of cell wall are made inside the existing hoops before bonds are cleaved. Division can occur, however, when a constrictive force brings the midcell into a compressed state before new hoops of relaxed cell wall are incorporated between existing hoops. Adding a make-before-break mechanism drives division with a smaller constrictive force sufficient to bring the midcell into a relaxed, but not necessarily compressed, state.
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Affiliation(s)
- Lam T Nguyen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - H Jane Ding
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, 422 Curie Boulevard, Philadelphia, PA, 19104, USA
| | - Morgan Beeby
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA
- Department of Life Sciences, Imperial College London, South Kensington Campus, London, SW7 2AZ, UK
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, 1200 E. California Boulevard, Pasadena, CA, 91125, USA.
- Howard Hughes Medical Institute, 1200 E. California Boulevard, Pasadena, CA, 91125, USA.
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Abstract
In biology, function arises from form. For bacterial secretion systems, which often span two membranes, avidly bind to the cell wall, and contain hundreds of individual proteins, studying form is a daunting task, made possible by electron cryotomography (ECT). ECT is the highest-resolution imaging technique currently available to visualize unique objects inside cells, providing a three-dimensional view of the shapes and locations of large macromolecular complexes in their native environment. Over the past 15 years, ECT has contributed to the study of bacterial secretion systems in two main ways: by revealing intact forms for the first time and by mapping components into these forms. Here we highlight some of these contributions, revealing structural convergence in type II secretion systems, structural divergence in type III secretion systems, unexpected structures in type IV secretion systems, and unexpected mechanisms in types V and VI secretion systems. Together, they offer a glimpse into a world of fantastic forms-nanoscale rotors, needles, pumps, and dart guns-much of which remains to be explored.
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Affiliation(s)
- Catherine M. Oikonomou
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Grant J. Jensen
- Department of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
- Howard Hughes Medical Institute, Pasadena, CA, USA
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10
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Kaplan M, Ghosal D, Subramanian P, Oikonomou CM, Kjaer A, Pirbadian S, Ortega DR, Briegel A, El-Naggar MY, Jensen GJ. The presence and absence of periplasmic rings in bacterial flagellar motors correlates with stator type. eLife 2019; 8:43487. [PMID: 30648971 PMCID: PMC6375700 DOI: 10.7554/elife.43487] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 12/19/2018] [Indexed: 12/22/2022] Open
Abstract
The bacterial flagellar motor, a cell-envelope-embedded macromolecular machine that functions as a cellular propeller, exhibits significant structural variability between species. Different torque-generating stator modules allow motors to operate in different pH, salt or viscosity levels. How such diversity evolved is unknown. Here, we use electron cryo-tomography to determine the in situ macromolecular structures of three Gammaproteobacteria motors: Legionella pneumophila, Pseudomonas aeruginosa, and Shewanella oneidensis, providing the first views of intact motors with dual stator systems. Complementing our imaging with bioinformatics analysis, we find a correlation between the motor’s stator system and its structural elaboration. Motors with a single H+-driven stator have only the core periplasmic P- and L-rings; those with dual H+-driven stators have an elaborated P-ring; and motors with Na+ or Na+/H+-driven stators have both their P- and L-rings embellished. Our results suggest an evolution of structural elaboration that may have enabled pathogenic bacteria to colonize higher-viscosity environments in animal hosts. Bacteria are so small that for them, making their way through water is like swimming in roofing tar for us. In response, these organisms have evolved a molecular machine that helps them move in their environment. Named the bacterial flagellum, this complex assemblage of molecules is formed of three main parts: a motor that spans the inner and outer membranes of the cell, and then a ‘hook’ that connects to a long filament which extends outside the bacterium. More precisely, the motor is formed of the stator, an ion pump that stays still, and of a rotor that can spin. Different rings can also be present in the space between the inner and outer membranes (the periplasm) and surround these components. The stator uses ions to generate the energy that makes the rotor whirl. In turn, this movement sets the filament in motion, propelling the bacterium. Depending on where the bacteria live, the stator can use different types of ions. In addition, while many species have a single stator system per motor, some may have several stator systems for one motor: this may help the microorganisms move in different conditions. As microbes colonize environments with a different pH or viscosity, they constantly evolve new versions of the motor which are more suitable to their new surroundings. However, a part of the motor remains the same across species. Overall, it is still unclear how bacterial flagella evolve, but examining the structure of new motors can shed light upon this process. Here, Kaplan et al. combine a bioinformatics approach with an imaging technique known as electron cryo-tomography to dissect the structure of the flagellar motor of three species of bacteria with different stator systems, and compare these to known motors of the same class. The results reveal a correlation between the nature of the stator system and the presence of certain elements. Stators that use sodium ions, or both sodium and hydrogen ions, are associated with two periplasmic rings surrounding the conserved motor structure. These rings do not exist in motors with single hydrogen-driven stators. Motors with dual hydrogen-driven stators are, to some extent, an ‘intermediate state’, with only one of those rings present. As all the studied species currently exist, it is difficult to know which version of the motor is the most ancient, and which one has evolved more recently. Capturing the diversity of bacterial motors gives us insight into the evolutionary forces that shape complex molecular structures, which is essential to understand how life evolved on Earth. More practically, this knowledge may also help us design better nanomachines to power microscopic robots.
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Affiliation(s)
- Mohammed Kaplan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Poorna Subramanian
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Andreas Kjaer
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Sahand Pirbadian
- Department of Physics and Astronomy, Biological Sciences, and Chemistry, University of Southern California, Los Angeles, United States
| | - Davi R Ortega
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Ariane Briegel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States
| | - Mohamed Y El-Naggar
- Department of Physics and Astronomy, Biological Sciences, and Chemistry, University of Southern California, Los Angeles, United States
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, United States.,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, United States
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12
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Carter SD, Mageswaran SK, Farino ZJ, Mamede JI, Oikonomou CM, Hope TJ, Freyberg Z, Jensen GJ. Distinguishing signal from autofluorescence in cryogenic correlated light and electron microscopy of mammalian cells. J Struct Biol 2017; 201:15-25. [PMID: 29078993 DOI: 10.1016/j.jsb.2017.10.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [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: 04/12/2017] [Revised: 10/21/2017] [Accepted: 10/23/2017] [Indexed: 01/09/2023]
Abstract
In cryogenic correlated light and electron microscopy (cryo-CLEM), frozen targets of interest are identified and located on EM grids by fluorescence microscopy and then imaged at higher resolution by cryo-EM. Whilst working with these methods, we discovered that a variety of mammalian cells exhibit strong punctate autofluorescence when imaged under cryogenic conditions (80 K). Autofluorescence originated from multilamellar bodies (MLBs) and secretory granules. Here we describe a method to distinguish fluorescent protein tags from these autofluorescent sources based on the narrower emission spectrum of the former. The method is first tested on mitochondria and then applied to examine the ultrastructural variability of secretory granules within insulin-secreting pancreatic beta-cell-derived INS-1E cells.
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Affiliation(s)
- Stephen D Carter
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Shrawan K Mageswaran
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
| | - Zachary J Farino
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - João I Mamede
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | | | - Thomas J Hope
- Department of Cell and Molecular Biology, Northwestern University, Chicago, IL 60611, USA
| | - Zachary Freyberg
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, PA 15213, USA; Department of Cell Biology, University of Pittsburgh, PA 15213, USA.
| | - Grant J Jensen
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA; Howard Hughes Medical Institute (HHMI), California Institute of Technology, Pasadena, CA 91125, USA.
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13
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Briegel A, Oikonomou CM, Chang YW, Kjær A, Huang AN, Kim KW, Ghosal D, Nguyen HH, Kenny D, Ogorzalek Loo RR, Gunsalus RP, Jensen GJ. Morphology of the archaellar motor and associated cytoplasmic cone in Thermococcus kodakaraensis. EMBO Rep 2017; 18:1660-1670. [PMID: 28729461 DOI: 10.15252/embr.201744070] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/29/2017] [Accepted: 07/04/2017] [Indexed: 11/09/2022] Open
Abstract
Archaeal swimming motility is driven by archaella: rotary motors attached to long extracellular filaments. The structure of these motors, and particularly how they are anchored in the absence of a peptidoglycan cell wall, is unknown. Here, we use electron cryotomography to visualize the archaellar basal body in vivo in Thermococcus kodakaraensis KOD1. Compared to the homologous bacterial type IV pilus (T4P), we observe structural similarities as well as several unique features. While the position of the cytoplasmic ATPase appears conserved, it is not braced by linkages that extend upward through the cell envelope as in the T4P, but rather by cytoplasmic components that attach it to a large conical frustum up to 500 nm in diameter at its base. In addition to anchoring the lophotrichous bundle of archaella, the conical frustum associates with chemosensory arrays and ribosome-excluding material and may function as a polar organizing center for the coccoid cells.
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Affiliation(s)
- Ariane Briegel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andreas Kjær
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Audrey N Huang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ki Woo Kim
- School of Ecology and Environmental System, Kyungpook National University, Sangju, South Korea
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Hong H Nguyen
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Dorothy Kenny
- Department of Microbiology, Immunology and Molecular Genetics, The UCLA DOE Institute, University of California, Los Angeles, CA, USA
| | - Rachel R Ogorzalek Loo
- Department of Chemistry and Biochemistry, University of California, Los Angeles, CA, USA
| | - Robert P Gunsalus
- Department of Microbiology, Immunology and Molecular Genetics, The UCLA DOE Institute, University of California, Los Angeles, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA .,Howard Hughes Medical Institute, Pasadena, CA, USA
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14
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Yao Q, Jewett AI, Chang YW, Oikonomou CM, Beeby M, Iancu CV, Briegel A, Ghosal D, Jensen GJ. Short FtsZ filaments can drive asymmetric cell envelope constriction at the onset of bacterial cytokinesis. EMBO J 2017; 36:1577-1589. [PMID: 28438890 DOI: 10.15252/embj.201696235] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2016] [Revised: 03/17/2017] [Accepted: 03/23/2017] [Indexed: 11/09/2022] Open
Abstract
FtsZ, the bacterial homologue of eukaryotic tubulin, plays a central role in cell division in nearly all bacteria and many archaea. It forms filaments under the cytoplasmic membrane at the division site where, together with other proteins it recruits, it drives peptidoglycan synthesis and constricts the cell. Despite extensive study, the arrangement of FtsZ filaments and their role in division continue to be debated. Here, we apply electron cryotomography to image the native structure of intact dividing cells and show that constriction in a variety of Gram-negative bacterial cells, including Proteus mirabilis and Caulobacter crescentus, initiates asymmetrically, accompanied by asymmetric peptidoglycan incorporation and short FtsZ-like filament formation. These results show that a complete ring of FtsZ is not required for constriction and lead us to propose a model for FtsZ-driven division in which short dynamic FtsZ filaments can drive initial peptidoglycan synthesis and envelope constriction at the onset of cytokinesis, later increasing in length and number to encircle the division plane and complete constriction.
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Affiliation(s)
- Qing Yao
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Andrew I Jewett
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Yi-Wei Chang
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Morgan Beeby
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Cristina V Iancu
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Ariane Briegel
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Debnath Ghosal
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA, USA .,Howard Hughes Medical Institute, California Institute of Technology, Pasadena, CA, USA
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15
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Abstract
Electron cryotomography (ECT) provides three-dimensional views of macromolecular complexes inside cells in a native frozen-hydrated state. Over the last two decades, ECT has revealed the ultrastructure of cells in unprecedented detail. It has also allowed us to visualize the structures of macromolecular machines in their native context inside intact cells. In many cases, such machines cannot be purified intact for in vitro study. In other cases, the function of a structure is lost outside the cell, so that the mechanism can be understood only by observation in situ. In this review, we describe the technique and its history and provide examples of its power when applied to cell biology. We also discuss the integration of ECT with other techniques, including lower-resolution fluorescence imaging and higher-resolution atomic structure determination, to cover the full scale of cellular processes.
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Affiliation(s)
- Catherine M Oikonomou
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; ,
| | - Grant J Jensen
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, California 91125; , .,Howard Hughes Medical Institute, Pasadena, California 91125
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17
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Ding HJ, Oikonomou CM, Jensen GJ. The Caltech Tomography Database and Automatic Processing Pipeline. J Struct Biol 2015; 192:279-86. [PMID: 26087141 DOI: 10.1016/j.jsb.2015.06.016] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 06/11/2015] [Accepted: 06/13/2015] [Indexed: 10/23/2022]
Abstract
Here we describe the Caltech Tomography Database and automatic image processing pipeline, designed to process, store, display, and distribute electron tomographic data including tilt-series, sample information, data collection parameters, 3D reconstructions, correlated light microscope images, snapshots, segmentations, movies, and other associated files. Tilt-series are typically uploaded automatically during collection to a user's "Inbox" and processed automatically, but can also be entered and processed in batches via scripts or file-by-file through an internet interface. As with the video website YouTube, each tilt-series is represented on the browsing page with a link to the full record, a thumbnail image and a video icon that delivers a movie of the tomogram in a pop-out window. Annotation tools allow users to add notes and snapshots. The database is fully searchable, and sets of tilt-series can be selected and re-processed, edited, or downloaded to a personal workstation. The results of further processing and snapshots of key results can be recorded in the database, automatically linked to the appropriate tilt-series. While the database is password-protected for local browsing and searching, datasets can be made public and individual files can be shared with collaborators over the Internet. Together these tools facilitate high-throughput tomography work by both individuals and groups.
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Affiliation(s)
- H Jane Ding
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States
| | - Catherine M Oikonomou
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States
| | - Grant J Jensen
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, United States; Howard Hughes Medical Institute, United States.
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18
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Briegel A, Ortega DR, Huang A, Oikonomou CM, Gunsalus RP, Jensen GJ. Structural conservation of chemotaxis machinery across Archaea and Bacteria. Environ Microbiol Rep 2015; 7:414-9. [PMID: 25581459 PMCID: PMC4782749 DOI: 10.1111/1758-2229.12265] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2014] [Revised: 12/12/2014] [Accepted: 12/25/2014] [Indexed: 05/27/2023]
Abstract
Chemotaxis allows cells to sense and respond to their environment. In Bacteria, stimuli are detected by arrays of chemoreceptors that relay the signal to a two-component regulatory system. These arrays take the form of highly stereotyped super-lattices comprising hexagonally packed trimers-of-receptor-dimers networked by rings of histidine kinase and coupling proteins. This structure is conserved across chemotactic Bacteria, and between membrane-bound and cytoplasmic arrays, and gives rise to the highly cooperative, dynamic nature of the signalling system. The chemotaxis system, absent in eukaryotes, is also found in Archaea, where its structural details remain uncharacterized. Here we provide evidence that the chemotaxis machinery was not present in the last archaeal common ancestor, but rather was introduced in one of the waves of lateral gene transfer that occurred after the branching of Eukaryota but before the diversification of Euryarchaeota. Unlike in Bacteria, the chemotaxis system then evolved largely vertically in Archaea, with very few subsequent successful lateral gene transfer events. By electron cryotomography, we find that the structure of both membrane-bound and cytoplasmic chemoreceptor arrays is conserved between Bacteria and Archaea, suggesting the fundamental importance of this signalling architecture across diverse prokaryotic lifestyles.
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Affiliation(s)
- Ariane Briegel
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125
| | - Davi R. Ortega
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125
| | - Audrey Huang
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125
| | | | - Robert P. Gunsalus
- University of California Los Angeles, 609 Charles E. Young Dr. S., Los Angeles, CA 90095
| | - Grant J. Jensen
- California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125
- Howard Hughes Medical Institute, 1200 E. California Blvd., Pasadena, CA 91125
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19
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Briegel A, Wong ML, Hodges HL, Oikonomou CM, Piasta KN, Harris MJ, Fowler DJ, Thompson LK, Falke JJ, Kiessling LL, Jensen GJ. Correction to New Insights into Bacterial Chemoreceptor Array Structure and Assembly from Electron Cryotomography. Biochemistry 2014. [PMCID: PMC4204879 DOI: 10.1021/bi501167j] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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20
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Briegel A, Wong ML, Hodges HL, Oikonomou CM, Piasta KN, Harris MJ, Fowler DJ, Thompson LK, Falke JJ, Kiessling LL, Jensen GJ. New insights into bacterial chemoreceptor array structure and assembly from electron cryotomography. Biochemistry 2014; 53:1575-85. [PMID: 24580139 PMCID: PMC3985956 DOI: 10.1021/bi5000614] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Bacterial chemoreceptors cluster in highly ordered, cooperative, extended arrays with a conserved architecture, but the principles that govern array assembly remain unclear. Here we show images of cellular arrays as well as selected chemoreceptor complexes reconstituted in vitro that reveal new principles of array structure and assembly. First, in every case, receptors clustered in a trimers-of-dimers configuration, suggesting this is a highly favored fundamental building block. Second, these trimers-of-receptor dimers exhibited great versatility in the kinds of contacts they formed with each other and with other components of the signaling pathway, although only one architectural type occurred in native arrays. Third, the membrane, while it likely accelerates the formation of arrays, was neither necessary nor sufficient for lattice formation. Molecular crowding substituted for the stabilizing effect of the membrane and allowed cytoplasmic receptor fragments to form sandwiched lattices that strongly resemble the cytoplasmic chemoreceptor arrays found in some bacterial species. Finally, the effective determinant of array structure seemed to be CheA and CheW, which formed a "superlattice" of alternating CheA-filled and CheA-empty rings that linked receptor trimers-of-dimer units into their native hexagonal lattice. While concomitant overexpression of receptors, CheA, and CheW yielded arrays with native spacing, the CheA occupancy was lower and less ordered, suggesting that temporal and spatial coordination of gene expression driven by a single transcription factor may be vital for full order, or that array overgrowth may trigger a disassembly process. The results described here provide new insights into the assembly intermediates and assembly mechanism of this massive macromolecular complex.
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Affiliation(s)
- Ariane Briegel
- Division of Biology, California Institute of Technology , 1200 East California Boulevard, Pasadena, California 91125, United States
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21
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Briegel A, Ames P, Gumbart JC, Oikonomou CM, Parkinson JS, Jensen GJ. The mobility of two kinase domains in the Escherichia coli chemoreceptor array varies with signalling state. Mol Microbiol 2013; 89:831-41. [PMID: 23802570 DOI: 10.1111/mmi.12309] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/24/2013] [Indexed: 11/30/2022]
Abstract
Motile bacteria sense their physical and chemical environment through highly cooperative, ordered arrays of chemoreceptors. These signalling complexes phosphorylate a response regulator which in turn governs flagellar motor reversals, driving cells towards favourable environments. The structural changes that translate chemoeffector binding into the appropriate kinase output are not known. Here, we apply high-resolution electron cryotomography to visualize mutant chemoreceptor signalling arrays in well-defined kinase activity states. The arrays were well ordered in all signalling states, with no discernible differences in receptor conformation at 2-3 nm resolution. Differences were observed, however, in a keel-like density that we identify here as CheA kinase domains P1 and P2, the phosphorylation site domain and the binding domain for response regulator target proteins. Mutant receptor arrays with high kinase activities all exhibited small keels and high proteolysis susceptibility, indicative of mobile P1 and P2 domains. In contrast, arrays in kinase-off signalling states exhibited a range of keel sizes. These findings confirm that chemoreceptor arrays do not undergo large structural changes during signalling, and suggest instead that kinase activity is modulated at least in part by changes in the mobility of key domains.
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Affiliation(s)
- Ariane Briegel
- California Institute of Technology, 1200 E. California Blvd, Pasadena, CA, 91125, USA
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