101
|
Chaikeeratisak V, Khanna K, Nguyen KT, Sugie J, Egan ME, Erb ML, Vavilina A, Nonejuie P, Nieweglowska E, Pogliano K, Agard DA, Villa E, Pogliano J. Viral Capsid Trafficking along Treadmilling Tubulin Filaments in Bacteria. Cell 2019; 177:1771-1780.e12. [PMID: 31199917 PMCID: PMC7301877 DOI: 10.1016/j.cell.2019.05.032] [Citation(s) in RCA: 46] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 01/24/2019] [Accepted: 05/17/2019] [Indexed: 12/13/2022]
Abstract
Cargo trafficking along microtubules is exploited by eukaryotic viruses, but no such examples have been reported in bacteria. Several large Pseudomonas phages assemble a dynamic, tubulin-based (PhuZ) spindle that centers replicating phage DNA sequestered within a nucleus-like structure. Here, we show that capsids assemble on the membrane and then move rapidly along PhuZ filaments toward the phage nucleus for DNA packaging. The spindle rotates the phage nucleus, distributing capsids around its surface. PhuZ filaments treadmill toward the nucleus at a constant rate similar to the rate of capsid movement and the linear velocity of nucleus rotation. Capsids become trapped along mutant static PhuZ filaments that are defective in GTP hydrolysis. Our results suggest a transport and distribution mechanism in which capsids attached to the sides of filaments are trafficked to the nucleus by PhuZ polymerization at the poles, demonstrating that the phage cytoskeleton evolved cargo-trafficking capabilities in bacteria.
Collapse
Affiliation(s)
- Vorrapon Chaikeeratisak
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA; Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Katrina T Nguyen
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - MacKennon E Egan
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Marcella L Erb
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Anastasia Vavilina
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Nakhon Pathom 73170, Thailand
| | - Eliza Nieweglowska
- Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA
| | - David A Agard
- Department of Biochemistry and Biophysics and the Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Elizabeth Villa
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA.
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, San Diego, CA 92093, USA.
| |
Collapse
|
102
|
Lopez-Garrido J, Ojkic N, Khanna K, Wagner FR, Villa E, Endres RG, Pogliano K. Chromosome Translocation Inflates Bacillus Forespores and Impacts Cellular Morphology. Cell 2019; 172:758-770.e14. [PMID: 29425492 DOI: 10.1016/j.cell.2018.01.027] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/16/2017] [Accepted: 01/18/2018] [Indexed: 01/14/2023]
Abstract
The means by which the physicochemical properties of different cellular components together determine bacterial cell shape remain poorly understood. Here, we investigate a programmed cell-shape change during Bacillus subtilis sporulation, when a rod-shaped vegetative cell is transformed to an ovoid spore. Asymmetric cell division generates a bigger mother cell and a smaller, hemispherical forespore. The septum traps the forespore chromosome, which is translocated to the forespore by SpoIIIE. Simultaneously, forespore size increases as it is reshaped into an ovoid. Using genetics, timelapse microscopy, cryo-electron tomography, and mathematical modeling, we demonstrate that forespore growth relies on membrane synthesis and SpoIIIE-mediated chromosome translocation, but not on peptidoglycan or protein synthesis. Our data suggest that the hydrated nucleoid swells and inflates the forespore, displacing ribosomes to the cell periphery, stretching septal peptidoglycan, and reshaping the forespore. Our results illustrate how simple biophysical interactions between core cellular components contribute to cellular morphology.
Collapse
Affiliation(s)
- Javier Lopez-Garrido
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Nikola Ojkic
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; Centre for Integrative Systems Biology and Bioinformatics, London SW7 2AZ, UK
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Felix R Wagner
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Robert G Endres
- Department of Life Sciences, Imperial College, London SW7 2AZ, UK; Centre for Integrative Systems Biology and Bioinformatics, London SW7 2AZ, UK.
| | - Kit Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
103
|
|
104
|
Structural studies of Acidianus tailed spindle virus reveal a structural paradigm used in the assembly of spindle-shaped viruses. Proc Natl Acad Sci U S A 2018; 115:2120-2125. [PMID: 29440399 DOI: 10.1073/pnas.1719180115] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The spindle-shaped virion morphology is common among archaeal viruses, where it is a defining characteristic of many viral families. However, structural heterogeneity intrinsic to spindle-shaped viruses has seriously hindered efforts to elucidate the molecular architecture of these lemon-shaped capsids. We have utilized a combination of cryo-electron microscopy and X-ray crystallography to study Acidianus tailed spindle virus (ATSV). These studies reveal the architectural principles that underlie assembly of a spindle-shaped virus. Cryo-electron tomography shows a smooth transition from the spindle-shaped capsid into the tubular-shaped tail and allows low-resolution structural modeling of individual virions. Remarkably, higher-dose 2D micrographs reveal a helical surface lattice in the spindle-shaped capsid. Consistent with this, crystallographic studies of the major capsid protein reveal a decorated four-helix bundle that packs within the crystal to form a four-start helical assembly with structural similarity to the tube-shaped tail structure of ATSV and other tailed, spindle-shaped viruses. Combined, this suggests that the spindle-shaped morphology of the ATSV capsid is formed by a multistart helical assembly with a smoothly varying radius and allows construction of a pseudoatomic model for the lemon-shaped capsid that extends into a tubular tail. The potential advantages that this novel architecture conveys to the life cycle of spindle-shaped viruses, including a role in DNA ejection, are discussed.
Collapse
|
105
|
Guo Q, Lehmer C, Martínez-Sánchez A, Rudack T, Beck F, Hartmann H, Pérez-Berlanga M, Frottin F, Hipp MS, Hartl FU, Edbauer D, Baumeister W, Fernández-Busnadiego R. In Situ Structure of Neuronal C9orf72 Poly-GA Aggregates Reveals Proteasome Recruitment. Cell 2018; 172:696-705.e12. [PMID: 29398115 PMCID: PMC6035389 DOI: 10.1016/j.cell.2017.12.030] [Citation(s) in RCA: 254] [Impact Index Per Article: 42.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Revised: 11/07/2017] [Accepted: 12/20/2017] [Indexed: 12/13/2022]
Abstract
Protein aggregation and dysfunction of the ubiquitin-proteasome system are hallmarks of many neurodegenerative diseases. Here, we address the elusive link between these phenomena by employing cryo-electron tomography to dissect the molecular architecture of protein aggregates within intact neurons at high resolution. We focus on the poly-Gly-Ala (poly-GA) aggregates resulting from aberrant translation of an expanded GGGGCC repeat in C9orf72, the most common genetic cause of amyotrophic lateral sclerosis and frontotemporal dementia. We find that poly-GA aggregates consist of densely packed twisted ribbons that recruit numerous 26S proteasome complexes, while other macromolecules are largely excluded. Proximity to poly-GA ribbons stabilizes a transient substrate-processing conformation of the 26S proteasome, suggesting stalled degradation. Thus, poly-GA aggregates may compromise neuronal proteostasis by driving the accumulation and functional impairment of a large fraction of cellular proteasomes.
Collapse
Affiliation(s)
- Qiang Guo
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Carina Lehmer
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Antonio Martínez-Sánchez
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Till Rudack
- Department of Biophysics, Ruhr University Bochum, 44780 Bochum, Germany; NIH Center for Macromolecular Modeling and Bioinformatics, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Champaign, IL 61801, USA
| | - Florian Beck
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Hannelore Hartmann
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Manuela Pérez-Berlanga
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Frédéric Frottin
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Mark S Hipp
- Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany; Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - F Ulrich Hartl
- Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany; Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Dieter Edbauer
- German Center for Neurodegenerative Diseases (DZNE), 81377 Munich, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany; Ludwig-Maximilians University Munich, 81377 Munich, Germany.
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - Rubén Fernández-Busnadiego
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| |
Collapse
|
106
|
Mickoleit F, Borkner CB, Toro-Nahuelpan M, Herold HM, Maier DS, Plitzko JM, Scheibel T, Schüler D. In Vivo Coating of Bacterial Magnetic Nanoparticles by Magnetosome Expression of Spider Silk-Inspired Peptides. Biomacromolecules 2018; 19:962-972. [PMID: 29357230 DOI: 10.1021/acs.biomac.7b01749] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Magnetosomes are natural magnetic nanoparticles with exceptional properties that are synthesized in magnetotactic bacteria by a highly regulated biomineralization process. Their usability in many applications could be further improved by encapsulation in biocompatible polymers. In this study, we explored the production of spider silk-inspired peptides on magnetosomes of the alphaproteobacterium Magnetospirillum gryphiswaldense. Genetic fusion of different silk sequence-like variants to abundant magnetosome membrane proteins enhanced magnetite biomineralization and caused the formation of a proteinaceous capsule, which increased the colloidal stability of isolated particles. Furthermore, we show that spider silk peptides fused to a magnetosome membrane protein can be used as seeds for silk fibril growth on the magnetosome surface. In summary, we demonstrate that the combination of two different biogenic materials generates a genetically encoded hybrid composite with engineerable new properties and enhanced potential for various applications.
Collapse
Affiliation(s)
| | | | - Mauricio Toro-Nahuelpan
- Department of Molecular Structural Biology , Max Planck Institute of Biochemistry , D-82152 Martinsried , Germany
| | | | | | - Jürgen M Plitzko
- Department of Molecular Structural Biology , Max Planck Institute of Biochemistry , D-82152 Martinsried , Germany
| | | | | |
Collapse
|
107
|
Ali RA, Mehdi AM, Rothnagel R, Hamilton NA, Gerle C, Landsberg MJ, Hankamer B. RAZA: A Rapid 3D z-crossings algorithm to segment electron tomograms and extract organelles and macromolecules. J Struct Biol 2017; 200:73-86. [PMID: 29032142 DOI: 10.1016/j.jsb.2017.10.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 10/06/2017] [Accepted: 10/09/2017] [Indexed: 11/30/2022]
Abstract
Resolving the 3D architecture of cells to atomic resolution is one of the most ambitious challenges of cellular and structural biology. Central to this process is the ability to automate tomogram segmentation to identify sub-cellular components, facilitate molecular docking and annotate detected objects with associated metadata. Here we demonstrate that RAZA (Rapid 3D z-crossings algorithm) provides a robust, accurate, intuitive, fast, and generally applicable segmentation algorithm capable of detecting organelles, membranes, macromolecular assemblies and extrinsic membrane protein domains. RAZA defines each continuous contour within a tomogram as a discrete object and extracts a set of 3D structural fingerprints (major, middle and minor axes, surface area and volume), enabling selective, semi-automated segmentation and object extraction. RAZA takes advantage of the fact that the underlying algorithm is a true 3D edge detector, allowing the axes of a detected object to be defined, independent of its random orientation within a cellular tomogram. The selectivity of object segmentation and extraction can be controlled by specifying a user-defined detection tolerance threshold for each fingerprint parameter, within which segmented objects must fall and/or by altering the number of search parameters, to define morphologically similar structures. We demonstrate the capability of RAZA to selectively extract subgroups of organelles (mitochondria) and macromolecular assemblies (ribosomes) from cellular tomograms. Furthermore, the ability of RAZA to define objects and their contours, provides a basis for molecular docking and rapid tomogram annotation.
Collapse
Affiliation(s)
- Rubbiya A Ali
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Ahmed M Mehdi
- Translational Research Institute, University of Queensland Diamantina Institute, Brisbane, QLD, Australia; Department of Electrical Engineering, University of Engineering and Technology, Lahore, Punjab, Pakistan
| | - Rosalba Rothnagel
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Nicholas A Hamilton
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia
| | - Christoph Gerle
- Picobiology Institute, Department of Life Science, Graduate School of Life Science, University of Hyogo, Kamigori, Japan; Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Japan
| | - Michael J Landsberg
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia; School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | - Ben Hankamer
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia.
| |
Collapse
|
108
|
Bäuerlein FJB, Saha I, Mishra A, Kalemanov M, Martínez-Sánchez A, Klein R, Dudanova I, Hipp MS, Hartl FU, Baumeister W, Fernández-Busnadiego R. In Situ Architecture and Cellular Interactions of PolyQ Inclusions. Cell 2017; 171:179-187.e10. [PMID: 28890085 DOI: 10.1016/j.cell.2017.08.009] [Citation(s) in RCA: 214] [Impact Index Per Article: 30.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/30/2017] [Accepted: 08/07/2017] [Indexed: 02/06/2023]
Abstract
Expression of many disease-related aggregation-prone proteins results in cytotoxicity and the formation of large intracellular inclusion bodies. To gain insight into the role of inclusions in pathology and the in situ structure of protein aggregates inside cells, we employ advanced cryo-electron tomography methods to analyze the structure of inclusions formed by polyglutamine (polyQ)-expanded huntingtin exon 1 within their intact cellular context. In primary mouse neurons and immortalized human cells, polyQ inclusions consist of amyloid-like fibrils that interact with cellular endomembranes, particularly of the endoplasmic reticulum (ER). Interactions with these fibrils lead to membrane deformation, the local impairment of ER organization, and profound alterations in ER membrane dynamics at the inclusion periphery. These results suggest that aberrant interactions between fibrils and endomembranes contribute to the deleterious cellular effects of protein aggregation. VIDEO ABSTRACT.
Collapse
Affiliation(s)
- Felix J B Bäuerlein
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Itika Saha
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Archana Mishra
- Department of Molecules, Signaling, and Development, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
| | - Maria Kalemanov
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Graduate School of Quantitative Biosciences Munich, 81337 Munich, Germany
| | - Antonio Martínez-Sánchez
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| | - Rüdiger Klein
- Department of Molecules, Signaling, and Development, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - Irina Dudanova
- Department of Molecules, Signaling, and Development, Max Planck Institute of Neurobiology, 82152 Martinsried, Germany
| | - Mark S Hipp
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany
| | - F Ulrich Hartl
- Department of Cellular Biochemistry, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany; Munich Cluster for Systems Neurology (SyNergy), 80336 Munich, Germany.
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany.
| | - Rubén Fernández-Busnadiego
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, 82152 Martinsried, Germany
| |
Collapse
|
109
|
Abstract
Underwater dam crack detection and classification based on sonar images is a challenging task because underwater environments are complex and because cracks are quite random and diverse in nature. Furthermore, obtainable sonar images are of low resolution. To address these problems, a novel underwater dam crack detection and classification approach based on sonar imagery is proposed. First, the sonar images are divided into image blocks. Second, a clustering analysis of a 3-D feature space is used to obtain the crack fragments. Third, the crack fragments are connected using an improved tensor voting method. Fourth, a minimum spanning tree is used to obtain the crack curve. Finally, an improved evidence theory combined with fuzzy rule reasoning is proposed to classify the cracks. Experimental results show that the proposed approach is able to detect underwater dam cracks and classify them accurately and effectively under complex underwater environments.
Collapse
Affiliation(s)
- Pengfei Shi
- College of IOT Engineering, Hohai University, Changzhou, Jiangsu, China
- * E-mail:
| | - Xinnan Fan
- College of IOT Engineering, Hohai University, Changzhou, Jiangsu, China
| | - Jianjun Ni
- College of IOT Engineering, Hohai University, Changzhou, Jiangsu, China
| | - Zubair Khan
- College of IOT Engineering, Hohai University, Changzhou, Jiangsu, China
| | - Min Li
- College of IOT Engineering, Hohai University, Changzhou, Jiangsu, China
| |
Collapse
|
110
|
Boedeker C, Schüler M, Reintjes G, Jeske O, van Teeseling MCF, Jogler M, Rast P, Borchert D, Devos DP, Kucklick M, Schaffer M, Kolter R, van Niftrik L, Engelmann S, Amann R, Rohde M, Engelhardt H, Jogler C. Determining the bacterial cell biology of Planctomycetes. Nat Commun 2017; 8:14853. [PMID: 28393831 PMCID: PMC5394234 DOI: 10.1038/ncomms14853] [Citation(s) in RCA: 129] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Accepted: 02/07/2017] [Indexed: 02/08/2023] Open
Abstract
Bacteria of the phylum Planctomycetes have been previously reported to possess several features that are typical of eukaryotes, such as cytosolic compartmentalization and endocytosis-like macromolecule uptake. However, recent evidence points towards a Gram-negative cell plan for Planctomycetes, although in-depth experimental analysis has been hampered by insufficient genetic tools. Here we develop methods for expression of fluorescent proteins and for gene deletion in a model planctomycete, Planctopirus limnophila, to analyse its cell organization in detail. Super-resolution light microscopy of mutants, cryo-electron tomography, bioinformatic predictions and proteomic analyses support an altered Gram-negative cell plan for Planctomycetes, including a defined outer membrane, a periplasmic space that can be greatly enlarged and convoluted, and an energized cytoplasmic membrane. These conclusions are further supported by experiments performed with two other Planctomycetes, Gemmata obscuriglobus and Rhodopirellula baltica. We also provide experimental evidence that is inconsistent with endocytosis-like macromolecule uptake; instead, extracellular macromolecules can be taken up and accumulate in the periplasmic space through unclear mechanisms.
Collapse
Affiliation(s)
| | - Margarete Schüler
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Greta Reintjes
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Olga Jeske
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Muriel C. F. van Teeseling
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands
- Department of Cellular Microbiology, Philipps-University Marburg, Faculty of Biology, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
| | - Mareike Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Patrick Rast
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Daniela Borchert
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
| | - Damien P. Devos
- Department of Cell biology and Biotechnology, CABD, Pablo de Olavide University-CSIC, Carretera de Utrera km1, 41013 Sevilla, Spain
| | - Martin Kucklick
- Helmholtz Center for Infection Research GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Department of Microbial Proteomics, Technical University Braunschweig, Institute for Microbiology, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Roberto Kolter
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, Massachusetts, 02115, USA
| | - Laura van Niftrik
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands
| | - Susanne Engelmann
- Helmholtz Center for Infection Research GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Department of Microbial Proteomics, Technical University Braunschweig, Institute for Microbiology, Spielmannstraße 7, 38106 Braunschweig, Germany
| | - Rudolf Amann
- Department of Molecular Ecology, Max Planck Institute for Marine Microbiology, Celsiusstraße 1, 28359 Bremen, Germany
| | - Manfred Rohde
- Helmholtz Center for Infection Research GmbH, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Harald Engelhardt
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Christian Jogler
- Leibniz Institute DSMZ, Inhoffenstraße 7b, 38124 Braunschweig, Germany
- Department of Microbiology, Radboud University, Heyendaalseweg 135, NL-6525 AJ Nijmegen, Netherlands
| |
Collapse
|
111
|
Cárdenes R, Zhang C, Klementieva O, Werner S, Guttmann P, Pratsch C, Cladera J, Bijnens BH. 3D membrane segmentation and quantification of intact thick cells using cryo soft X-ray transmission microscopy: A pilot study. PLoS One 2017; 12:e0174324. [PMID: 28376110 PMCID: PMC5380311 DOI: 10.1371/journal.pone.0174324] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2016] [Accepted: 03/07/2017] [Indexed: 12/28/2022] Open
Abstract
Structural analysis of biological membranes is important for understanding cell and sub-cellular organelle function as well as their interaction with the surrounding environment. Imaging of whole cells in three dimension at high spatial resolution remains a significant challenge, particularly for thick cells. Cryo-transmission soft X-ray microscopy (cryo-TXM) has recently gained popularity to image, in 3D, intact thick cells (∼10μm) with details of sub-cellular architecture and organization in near-native state. This paper reports a new tool to segment and quantify structural changes of biological membranes in 3D from cryo-TXM images by tracking an initial 2D contour along the third axis of the microscope, through a multi-scale ridge detection followed by an active contours-based model, with a subsequent refinement along the other two axes. A quantitative metric that assesses the grayscale profiles perpendicular to the membrane surfaces is introduced and shown to be linearly related to the membrane thickness. Our methodology has been validated on synthetic phantoms using realistic microscope properties and structure dimensions, as well as on real cryo-TXM data. Results demonstrate the validity of our algorithms for cryo-TXM data analysis.
Collapse
Affiliation(s)
| | - Chong Zhang
- Physense, Universitat Pompeu Fabra, Barcelona, Spain
| | - Oxana Klementieva
- Institute of Neuropathology, IDIBELL-University Hospital Bellvitge, L’Hospitalet de Llobregat, Spain
- Experimental Dementia Research Unit, Department of Experimental Medical Science, Lund University, Lund, Sweden
| | - Stephan Werner
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute Soft Matters and Functional Materials, Electron Storage Ring BESSY II, Berlin, Germany
| | - Peter Guttmann
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute Soft Matters and Functional Materials, Electron Storage Ring BESSY II, Berlin, Germany
| | - Christoph Pratsch
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Institute Soft Matters and Functional Materials, Electron Storage Ring BESSY II, Berlin, Germany
| | - Josep Cladera
- Biophysics Unit & Centre of Studies in Biophysics, Dept. of Biochemistry & Molecular Biology, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Bart H. Bijnens
- Physense, Universitat Pompeu Fabra, Barcelona, Spain
- ICREA, Barcelona, Spain
- * E-mail:
| |
Collapse
|
112
|
Earnest TM, Watanabe R, Stone JE, Mahamid J, Baumeister W, Villa E, Luthey-Schulten Z. Challenges of Integrating Stochastic Dynamics and Cryo-Electron Tomograms in Whole-Cell Simulations. J Phys Chem B 2017; 121:3871-3881. [PMID: 28291359 DOI: 10.1021/acs.jpcb.7b00672] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cryo-electron tomography (cryo-ET) has rapidly emerged as a powerful tool to investigate the internal, three-dimensional spatial organization of the cell. In parallel, the GPU-based technology to perform spatially resolved stochastic simulations of whole cells has arisen, allowing the simulation of complex biochemical networks over cell cycle time scales using data taken from -omics, single molecule experiments, and in vitro kinetics. By using real cell geometry derived from cryo-ET data, we have the opportunity to imbue these highly detailed structural data-frozen in time-with realistic biochemical dynamics and investigate how cell structure affects the behavior of the embedded chemical reaction network. Here we present two examples to illustrate the challenges and techniques involved in integrating structural data into stochastic simulations. First, a tomographic reconstruction of Saccharomyces cerevisiae is used to construct the geometry of an entire cell through which a simple stochastic model of an inducible genetic switch is studied. Second, a tomogram of the nuclear periphery in a HeLa cell is converted directly to the simulation geometry through which we study the effects of cellular substructure on the stochastic dynamics of gene repression. These simple chemical models allow us to illustrate how to build whole-cell simulations using cryo-ET derived geometry and the challenges involved in such a process.
Collapse
Affiliation(s)
- Tyler M Earnest
- National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States.,Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States
| | - Reika Watanabe
- Department of Chemistry and Biochemistry, University of California , San Diego, California, United States
| | - John E Stone
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States
| | - Julia Mahamid
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry , Munich, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry , Munich, Germany
| | - Elizabeth Villa
- Department of Chemistry and Biochemistry, University of California , San Diego, California, United States
| | - Zaida Luthey-Schulten
- Department of Chemistry, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States.,Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign , Urbana, Illinois, United States
| |
Collapse
|
113
|
Pfeffer S, Dudek J, Schaffer M, Ng BG, Albert S, Plitzko JM, Baumeister W, Zimmermann R, Freeze HH, Engel BD, Förster F. Dissecting the molecular organization of the translocon-associated protein complex. Nat Commun 2017; 8:14516. [PMID: 28218252 PMCID: PMC5321747 DOI: 10.1038/ncomms14516] [Citation(s) in RCA: 102] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 01/05/2017] [Indexed: 12/26/2022] Open
Abstract
In eukaryotic cells, one-third of all proteins must be transported across or inserted into the endoplasmic reticulum (ER) membrane by the ER protein translocon. The translocon-associated protein (TRAP) complex is an integral component of the translocon, assisting the Sec61 protein-conducting channel by regulating signal sequence and transmembrane helix insertion in a substrate-dependent manner. Here we use cryo-electron tomography (CET) to study the structure of the native translocon in evolutionarily divergent organisms and disease-linked TRAP mutant fibroblasts from human patients. The structural differences detected by subtomogram analysis form a basis for dissecting the molecular organization of the TRAP complex. We assign positions to the four TRAP subunits within the complex, providing insights into their individual functions. The revealed molecular architecture of a central translocon component advances our understanding of membrane protein biogenesis and sheds light on the role of TRAP in human congenital disorders of glycosylation.
Collapse
Affiliation(s)
- Stefan Pfeffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Johanna Dudek
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Building 44, 66421 Homburg, Germany
| | - Miroslava Schaffer
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Bobby G Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Sahradha Albert
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Richard Zimmermann
- Department of Medical Biochemistry and Molecular Biology, Saarland University, Building 44, 66421 Homburg, Germany
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, 10901 North Torrey Pines Road, La Jolla, California 92037, USA
| | - Benjamin D Engel
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Friedrich Förster
- Department of Molecular Structural Biology, Max-Planck Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.,Cryo-Electron Microscopy, Bijvoet Center for Biomolecular Research, Department of Chemistry, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
114
|
Hoang TV, Kizilyaprak C, Spehner D, Humbel BM, Schultz P. Automatic segmentation of high pressure frozen and freeze-substituted mouse retina nuclei from FIB-SEM tomograms. J Struct Biol 2017; 197:123-134. [DOI: 10.1016/j.jsb.2016.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Revised: 10/03/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
|
115
|
Chaikeeratisak V, Nguyen K, Khanna K, Brilot AF, Erb ML, Coker JKC, Vavilina A, Newton GL, Buschauer R, Pogliano K, Villa E, Agard DA, Pogliano J. Assembly of a nucleus-like structure during viral replication in bacteria. Science 2017; 355:194-197. [PMID: 28082593 PMCID: PMC6028185 DOI: 10.1126/science.aal2130] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/15/2016] [Indexed: 01/01/2023]
Abstract
We observed the assembly of a nucleus-like structure in bacteria during viral infection. Using fluorescence microscopy and cryo-electron tomography, we showed that Pseudomonas chlororaphis phage 201φ2-1 assembled a compartment that separated viral DNA from the cytoplasm. The phage compartment was centered by a bipolar tubulin-based spindle, and it segregated phage and bacterial proteins according to function. Proteins involved in DNA replication and transcription localized inside the compartment, whereas proteins involved in translation and nucleotide synthesis localized outside. Later during infection, viral capsids assembled on the cytoplasmic membrane and moved to the surface of the compartment for DNA packaging. Ultimately, viral particles were released from the compartment and the cell lysed. These results demonstrate that phages have evolved a specialized structure to compartmentalize viral replication.
Collapse
Affiliation(s)
- Vorrapon Chaikeeratisak
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Katrina Nguyen
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Kanika Khanna
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Axel F Brilot
- Howard Hughes Medical Institute (HHMI) and the Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Marcella L Erb
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Joanna K C Coker
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Anastasia Vavilina
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Gerald L Newton
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Robert Buschauer
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - Kit Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA
| | - Elizabeth Villa
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, CA 92093, USA
| | - David A Agard
- Howard Hughes Medical Institute (HHMI) and the Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158, USA
| | - Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA 92093, USA.
| |
Collapse
|
116
|
Kaltdorf KV, Schulze K, Helmprobst F, Kollmannsberger P, Dandekar T, Stigloher C. FIJI Macro 3D ART VeSElecT: 3D Automated Reconstruction Tool for Vesicle Structures of Electron Tomograms. PLoS Comput Biol 2017; 13:e1005317. [PMID: 28056033 PMCID: PMC5289597 DOI: 10.1371/journal.pcbi.1005317] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 02/02/2017] [Accepted: 12/18/2016] [Indexed: 11/18/2022] Open
Abstract
Automatic image reconstruction is critical to cope with steadily increasing data from advanced microscopy. We describe here the Fiji macro 3D ART VeSElecT which we developed to study synaptic vesicles in electron tomograms. We apply this tool to quantify vesicle properties (i) in embryonic Danio rerio 4 and 8 days past fertilization (dpf) and (ii) to compare Caenorhabditis elegans N2 neuromuscular junctions (NMJ) wild-type and its septin mutant (unc-59(e261)). We demonstrate development-specific and mutant-specific changes in synaptic vesicle pools in both models. We confirm the functionality of our macro by applying our 3D ART VeSElecT on zebrafish NMJ showing smaller vesicles in 8 dpf embryos then 4 dpf, which was validated by manual reconstruction of the vesicle pool. Furthermore, we analyze the impact of C. elegans septin mutant unc-59(e261) on vesicle pool formation and vesicle size. Automated vesicle registration and characterization was implemented in Fiji as two macros (registration and measurement). This flexible arrangement allows in particular reducing false positives by an optional manual revision step. Preprocessing and contrast enhancement work on image-stacks of 1nm/pixel in x and y direction. Semi-automated cell selection was integrated. 3D ART VeSElecT removes interfering components, detects vesicles by 3D segmentation and calculates vesicle volume and diameter (spherical approximation, inner/outer diameter). Results are collected in color using the RoiManager plugin including the possibility of manual removal of non-matching confounder vesicles. Detailed evaluation considered performance (detected vesicles) and specificity (true vesicles) as well as precision and recall. We furthermore show gain in segmentation and morphological filtering compared to learning based methods and a large time gain compared to manual segmentation. 3D ART VeSElecT shows small error rates and its speed gain can be up to 68 times faster in comparison to manual annotation. Both automatic and semi-automatic modes are explained including a tutorial.
Collapse
Affiliation(s)
- Kristin Verena Kaltdorf
- Division of Electron Microscopy, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Katja Schulze
- Molecular Biotechnology and Functional Genomics, Technical University of Applied Sciences Wildau, Wildau, Germany
| | - Frederik Helmprobst
- Division of Electron Microscopy, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Philip Kollmannsberger
- Center for Computational and Theoretical Biology, University of Wuerzburg, Wuerzburg, Germany
| | - Thomas Dandekar
- Department of Bioinformatics, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- * E-mail: (TD); (CS)
| | - Christian Stigloher
- Division of Electron Microscopy, Biocenter, University of Wuerzburg, Wuerzburg, Germany
- * E-mail: (TD); (CS)
| |
Collapse
|
117
|
Toro-Nahuelpan M, Müller FD, Klumpp S, Plitzko JM, Bramkamp M, Schüler D. Segregation of prokaryotic magnetosomes organelles is driven by treadmilling of a dynamic actin-like MamK filament. BMC Biol 2016; 14:88. [PMID: 27733152 PMCID: PMC5059902 DOI: 10.1186/s12915-016-0290-1] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2016] [Accepted: 07/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The navigation of magnetotactic bacteria relies on specific intracellular organelles, the magnetosomes, which are membrane-enclosed crystals of magnetite aligned into a linear chain. The magnetosome chain acts as a cellular compass, aligning the cells in the geomagnetic field in order to search for suitable environmental conditions in chemically stratified water columns and sediments. During cytokinesis, magnetosome chains have to be properly positioned, cleaved and separated in order to be evenly passed into daughter cells. In Magnetospirillum gryphiswaldense, the assembly of the magnetosome chain is controlled by the actin-like MamK, which polymerizes into cytoskeletal filaments that are connected to magnetosomes through the acidic MamJ protein. MamK filaments were speculated to recruit the magnetosome chain to cellular division sites, thus ensuring equal organelle inheritance. However, the underlying mechanism of magnetic organelle segregation has remained largely unknown. RESULTS Here, we performed in vivo time-lapse fluorescence imaging to directly track the intracellular movement and dynamics of magnetosome chains as well as photokinetic and ultrastructural analyses of the actin-like cytoskeletal MamK filament. We show that magnetosome chains undergo rapid intracellular repositioning from the new poles towards midcell into the newborn daughter cells, and the driving force for magnetosomes movement is likely provided by the pole-to-midcell treadmilling growth of MamK filaments. We further discovered that splitting and equipartitioning of magnetosome chains occurs with unexpectedly high accuracy, which depends directly on the dynamics of MamK filaments. CONCLUSION We propose a novel mechanism for prokaryotic organelle segregation that, similar to the type-II bacterial partitioning system of plasmids, relies on the action of cytomotive actin-like filaments together with specific connectors, which transport the magnetosome cargo in a fashion reminiscent of eukaryotic actin-organelle transport and segregation mechanisms.
Collapse
Affiliation(s)
- Mauricio Toro-Nahuelpan
- Department of Microbiology, University of Bayreuth, 95447, Bayreuth, Germany.,Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Planegg-Martinsried, Germany
| | - Frank D Müller
- Department of Microbiology, University of Bayreuth, 95447, Bayreuth, Germany
| | - Stefan Klumpp
- Department Theory and Bio-Systems, Max Planck Institute of Colloids and Interfaces, Potsdam, Germany.,Institute for Nonlinear Dynamics, Georg August University Göttingen, Göttingen, Germany
| | - Jürgen M Plitzko
- Department of Molecular Structural Biology, Max Planck Institute of Biochemistry, Planegg-Martinsried, Germany
| | - Marc Bramkamp
- Department of Biology I, Ludwig-Maximilians-University Munich, Planegg-Martinsried, Germany
| | - Dirk Schüler
- Department of Microbiology, University of Bayreuth, 95447, Bayreuth, Germany.
| |
Collapse
|
118
|
Lučić V, Fernández-Busnadiego R, Laugks U, Baumeister W. Hierarchical detection and analysis of macromolecular complexes in cryo-electron tomograms using Pyto software. J Struct Biol 2016; 196:503-514. [PMID: 27742578 DOI: 10.1016/j.jsb.2016.10.004] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 09/15/2016] [Accepted: 10/06/2016] [Indexed: 11/29/2022]
Abstract
Molecular complexes, arguably the basic units carrying cellular function, can be visualized directly in their native environment by cryo-electron tomography. Here we describe a procedure for the detection of small, pleomorphic membrane-bound molecular complexes in cryo-tomograms by a hierarchical connectivity segmentation. Validation on phantom and real data showed above 90% true positive rates. This segmentation procedure is implemented in the Pyto software package, together with methods for quantitative characterization and classification of complexes detected by our segmentation procedure and for statistical analysis between experimental conditions. Therefore, the methods presented provide a means for the detection and quantitative interpretation of structures captured in cryo-electron tomograms, as well as for the elucidation of their cellular function.
Collapse
Affiliation(s)
- Vladan Lučić
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany.
| | | | - Ulrike Laugks
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Wolfgang Baumeister
- Max-Planck-Institute of Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| |
Collapse
|
119
|
Fernandez-Fernandez MR, Ruiz-Garcia D, Martin-Solana E, Chichon FJ, Carrascosa JL, Fernandez JJ. 3D electron tomography of brain tissue unveils distinct Golgi structures that sequester cytoplasmic contents in neurons. J Cell Sci 2016; 130:83-89. [PMID: 27505890 DOI: 10.1242/jcs.188060] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Accepted: 07/27/2016] [Indexed: 12/12/2022] Open
Abstract
Macroautophagy is morphologically characterized by autophagosome formation. Autophagosomes are double-membraned vesicles that sequester cytoplasmic components for further degradation in the lysosome. Basal autophagy is paramount for intracellular quality control in post-mitotic cells but, surprisingly, the number of autophagosomes in post-mitotic neurons is very low, suggesting that alternative degradative structures could exist in neurons. To explore this possibility, we have examined neuronal subcellular architecture by performing three-dimensional (3D) electron tomography analysis of mouse brain tissue that had been preserved through high-pressure freezing. Here, we report that sequestration of neuronal cytoplasmic contents occurs at the Golgi complex in distinct and dynamic structures that coexist with autophagosomes in the brain. These structures are composed of several concentric double-membraned layers that appear to be formed simultaneously by the direct bending and sealing of discrete Golgi stacks. These structures are labelled for proteolytic enzymes, and lysosomes and late endosomes are found in contact with them, leading to the possibility that the sequestered material could be degraded inside them. Our findings highlight the key role that 3D electron tomography, together with tissue rapid-freezing techniques, will have in gaining new knowledge about subcellular architecture.
Collapse
Affiliation(s)
| | - Desire Ruiz-Garcia
- Macromolecular Structures Department, Centro Nacional de Biotecnología-CSIC, Darwin, 3, Cantoblanco, Madrid 28049, Spain
| | - Eva Martin-Solana
- Macromolecular Structures Department, Centro Nacional de Biotecnología-CSIC, Darwin, 3, Cantoblanco, Madrid 28049, Spain
| | - Francisco Javier Chichon
- Macromolecular Structures Department, Centro Nacional de Biotecnología-CSIC, Darwin, 3, Cantoblanco, Madrid 28049, Spain
| | - Jose L Carrascosa
- Macromolecular Structures Department, Centro Nacional de Biotecnología-CSIC, Darwin, 3, Cantoblanco, Madrid 28049, Spain
| | - Jose-Jesus Fernandez
- Macromolecular Structures Department, Centro Nacional de Biotecnología-CSIC, Darwin, 3, Cantoblanco, Madrid 28049, Spain
| |
Collapse
|
120
|
Genetic and Ultrastructural Analysis Reveals the Key Players and Initial Steps of Bacterial Magnetosome Membrane Biogenesis. PLoS Genet 2016; 12:e1006101. [PMID: 27286560 PMCID: PMC4902198 DOI: 10.1371/journal.pgen.1006101] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Accepted: 05/12/2016] [Indexed: 11/19/2022] Open
Abstract
Magnetosomes of magnetotactic bacteria contain well-ordered nanocrystals for magnetic navigation and have recently emerged as the most sophisticated model system to study the formation of membrane bounded organelles in prokaryotes. Magnetosome biosynthesis is thought to begin with the formation of a dedicated compartment, the magnetosome membrane (MM), in which the biosynthesis of a magnetic mineral is strictly controlled. While the biomineralization of magnetosomes and their subsequent assembly into linear chains recently have become increasingly well studied, the molecular mechanisms and early stages involved in MM formation remained poorly understood. In the Alphaproteobacterium Magnetospirillum gryphiswaldense, approximately 30 genes were found to control magnetosome biosynthesis. By cryo-electron tomography of several key mutant strains we identified the gene complement controlling MM formation in this model organism. Whereas the putative magnetosomal iron transporter MamB was most crucial for the process and caused the most severe MM phenotype upon elimination, MamM, MamQ and MamL were also required for the formation of wild-type-like MMs. A subset of seven genes (mamLQBIEMO) combined within a synthetic operon was sufficient to restore the formation of intracellular membranes in the absence of other genes from the key mamAB operon. Tracking of de novo magnetosome membrane formation by genetic induction revealed that magnetosomes originate from unspecific cytoplasmic membrane locations before alignment into coherent chains. Our results indicate that no single factor alone is essential for MM formation, which instead is orchestrated by the cumulative action of several magnetosome proteins. One of the most intriguing examples for membrane-bounded prokaryotic organelles are magnetosomes which consist of well-ordered chains of perfectly shaped magnetic nanocrystals that in many aquatic bacteria serve as geomagnetic field sensors to direct their swimming towards microoxic zones at the bottom of natural waters. In the model bacterium Magnetospirillum gryphiswaldense and related magnetotactic microorganisms, magnetosomes are formed by a complex pathway that is orchestrated by more than 30 genes. However, the initial and most crucial step of magnetosome biosynthesis, formation and differentiation of a dedicated intracellular membrane compartment for controlled biomineralization of magnetite crystals, remained only poorly understood. By ultrastructural analysis of several mutants and genetic induction of de novo magnetosome synthesis, we identified the key determinants and early steps of magnetosome membrane biogenesis. Our results suggest that formation of intracellular membranes in bacteria is mediated by a cumulative action of several factors, but apparently is differently controlled than intracellular membrane remodeling in eukaryotic cells.
Collapse
|
121
|
Fernández de Castro I, Fernández JJ, Barajas D, Nagy PD, Risco C. Three-dimensional imaging of the intracellular assembly of a functional viral RNA replicase complex. J Cell Sci 2016; 130:260-268. [PMID: 27026525 DOI: 10.1242/jcs.181586] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2015] [Accepted: 03/18/2016] [Indexed: 01/30/2023] Open
Abstract
Positive-strand RNA viruses, which can be devastating pathogens in humans, animals and plants, replicate their genomes on intracellular membranes. Here, we describe the three-dimensional ultrastructural organization of a tombusvirus replicase in yeast, a valuable model for exploring virus-host interactions. We visualized the intracellular distribution of a viral replicase protein using metal-tagging transmission electron microscopy, a highly sensitive nanotechnology whose full potential remains to be developed. These three-dimensional images show how viral replicase molecules are organized when they are incorporated into the active domains of the intracellular replication compartment. Our approach provides a means to study protein activation mechanisms in cells and to identify targets for new antiviral compounds.
Collapse
Affiliation(s)
- Isabel Fernández de Castro
- Cell Structure Laboratory, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid 28049, Spain
| | - José J Fernández
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid 28049, Spain
| | - Daniel Barajas
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, KY 40546, USA
| | - Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, KY 40546, USA
| | - Cristina Risco
- Cell Structure Laboratory, Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid 28049, Spain
| |
Collapse
|
122
|
Tasel SF, Mumcuoglu EU, Hassanpour RZ, Perkins G. A validated active contour method driven by parabolic arc model for detection and segmentation of mitochondria. J Struct Biol 2016; 194:253-71. [PMID: 26956730 DOI: 10.1016/j.jsb.2016.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2015] [Revised: 02/16/2016] [Accepted: 03/04/2016] [Indexed: 11/19/2022]
Abstract
Recent studies reveal that mitochondria take substantial responsibility in cellular functions that are closely related to aging diseases caused by degeneration of neurons. These studies emphasize that the membrane and crista morphology of a mitochondrion should receive attention in order to investigate the link between mitochondrial function and its physical structure. Electron microscope tomography (EMT) allows analysis of the inner structures of mitochondria by providing highly detailed visual data from large volumes. Computerized segmentation of mitochondria with minimum manual effort is essential to accelerate the study of mitochondrial structure/function relationships. In this work, we improved and extended our previous attempts to detect and segment mitochondria from transmission electron microcopy (TEM) images. A parabolic arc model was utilized to extract membrane structures. Then, curve energy based active contours were employed to obtain roughly outlined candidate mitochondrial regions. Finally, a validation process was applied to obtain the final segmentation data. 3D extension of the algorithm is also presented in this paper. Our method achieved an average F-score performance of 0.84. Average Dice Similarity Coefficient and boundary error were measured as 0.87 and 14nm respectively.
Collapse
Affiliation(s)
- Serdar F Tasel
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06531 Ankara, Turkey; Department of Computer Engineering, Cankaya University, 06810 Ankara, Turkey.
| | - Erkan U Mumcuoglu
- Department of Health Informatics, Graduate School of Informatics, Middle East Technical University, 06531 Ankara, Turkey
| | - Reza Z Hassanpour
- Department of Computer Engineering, Cankaya University, 06810 Ankara, Turkey
| | - Guy Perkins
- National Center for Microscopy and Imaging Research, University of California, San Diego, CA 92093-0608, USA
| |
Collapse
|
123
|
In Situ Cryo-Electron Tomography: A Post-Reductionist Approach to Structural Biology. J Mol Biol 2016; 428:332-343. [DOI: 10.1016/j.jmb.2015.09.030] [Citation(s) in RCA: 128] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 09/28/2015] [Accepted: 09/30/2015] [Indexed: 11/24/2022]
|
124
|
Page C, Hanein D, Volkmann N. Accurate membrane tracing in three-dimensional reconstructions from electron cryotomography data. Ultramicroscopy 2015; 155:20-26. [PMID: 25863868 DOI: 10.1016/j.ultramic.2015.03.021] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2014] [Revised: 03/19/2015] [Accepted: 03/27/2015] [Indexed: 01/19/2023]
Abstract
The connection between the extracellular matrix and the cell is of major importance for mechanotransduction and mechanobiology. Electron cryo-tomography, in principle, enables better than nanometer-resolution analysis of these connections, but restrictions of data collection geometry hamper the accurate extraction of the ventral membrane location from these tomograms, an essential prerequisite for the analysis. Here, we introduce a novel membrane tracing strategy that enables ventral membrane extraction at high fidelity and extraordinary accuracy. The approach is based on detecting the boundary between the inside and the outside of the cell rather than trying to explicitly trace the membrane. Simulation studies show that over 99% of the membrane can be correctly modeled using this principle and the excellent match of visually identifiable membrane stretches with the extracted boundary of experimental data indicates that the accuracy is comparable for actual data.
Collapse
Affiliation(s)
- Christopher Page
- Sanford-Burnham Medical Research Institute, Bioinformatics and Structural Biology Program, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Dorit Hanein
- Sanford-Burnham Medical Research Institute, Bioinformatics and Structural Biology Program, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Niels Volkmann
- Sanford-Burnham Medical Research Institute, Bioinformatics and Structural Biology Program, 10901 N Torrey Pines Rd, La Jolla, CA 92037, USA.
| |
Collapse
|