401
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Abstract
Electron cryotomography is an emerging technique that allows the structures of unique biological objects such as individual macromolecules, viruses, and even small whole cells to be reconstructed in their near-native states in three dimensions (3-D) to an approximate 5-nm resolution. The required instrumentation, sample preparation and limitations, data collection, typical results, and future prospects are summarized briefly.
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402
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Butan C, Winkler DC, Heymann JB, Craven RC, Steven AC. RSV capsid polymorphism correlates with polymerization efficiency and envelope glycoprotein content: implications that nucleation controls morphogenesis. J Mol Biol 2007; 376:1168-81. [PMID: 18206161 DOI: 10.1016/j.jmb.2007.12.003] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2007] [Revised: 11/30/2007] [Accepted: 12/04/2007] [Indexed: 01/12/2023]
Abstract
We used cryo-electron tomography to visualize Rous sarcoma virus, the prototypic alpharetrovirus. Its polyprotein Gag assembles into spherical procapsids, concomitant with budding. In maturation, Gag is dissected into its matrix, capsid protein (CA), and nucleocapsid moieties. CA reassembles into cores housing the viral RNA and replication enzymes. Evidence suggests that a correctly formed core is essential for infectivity. The virions in our data set range from approximately 105 to approximately 175 nm in diameter. Their cores are highly polymorphic. We observe angular cores, including some that are distinctively "coffin-shaped" for which we propose a novel fullerene geometry; cores with continuous curvature including, rarely, fullerene cones; and tubular cores. Angular cores are the most voluminous and densely packed; tubes and some curved cores contain less material, suggesting incomplete packaging. From the tomograms, we measured the surface areas of cores and, hence, their contents of CA subunits. From the virion diameters, we estimated their original complements of Gag. We find that Rous sarcoma virus virions, like the human immunodeficiency virus, contain unassembled CA subunits and that the fraction of CA that is assembled correlates with core type; angular cores incorporate approximately 80% of the available subunits, and open-ended tubes, approximately 30%. The number of glycoprotein spikes is variable (approximately 0 to 118) and also correlates with core type; virions with angular cores average 82 spikes, whereas those with tubular cores average 14 spikes. These observations imply that initiation of CA assembly, in which interactions of spike endodomains with the Gag layer play a role, is a critical determinant of core morphology.
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Affiliation(s)
- Carmen Butan
- Laboratory of Structural Biology, National Institute for Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
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403
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Li Z, Trimble MJ, Brun YV, Jensen GJ. The structure of FtsZ filaments in vivo suggests a force-generating role in cell division. EMBO J 2007; 26:4694-708. [PMID: 17948052 DOI: 10.1038/sj.emboj.7601895] [Citation(s) in RCA: 293] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2007] [Accepted: 09/26/2007] [Indexed: 11/10/2022] Open
Abstract
In prokaryotes, FtsZ (the filamentous temperature sensitive protein Z) is a nearly ubiquitous GTPase that localizes in a ring at the leading edge of constricting plasma membranes during cell division. Here we report electron cryotomographic reconstructions of dividing Caulobacter crescentus cells wherein individual arc-like filaments were resolved just underneath the inner membrane at constriction sites. The filaments' position, orientation, time of appearance, and resistance to A22 all suggested that they were FtsZ. Predictable changes in the number, length, and distribution of filaments in cells where the expression levels and stability of FtsZ were altered supported that conclusion. In contrast to the thick, closed-ring-like structure suggested by fluorescence light microscopy, throughout the constriction process the Z-ring was seen here to consist of just a few short (approximately 100 nm) filaments spaced erratically near the division site. Additional densities connecting filaments to the cell wall, occasional straight segments, and abrupt kinks were also seen. An 'iterative pinching' model is proposed wherein FtsZ itself generates the force that constricts the membrane in a GTP-hydrolysis-driven cycle of polymerization, membrane attachment, conformational change, depolymerization, and nucleotide exchange.
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Affiliation(s)
- Zhuo Li
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA
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404
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Hierro A, Rojas AL, Rojas R, Murthy N, Effantin G, Kajava AV, Steven AC, Bonifacino JS, Hurley JH. Functional architecture of the retromer cargo-recognition complex. Nature 2007; 449:1063-7. [PMID: 17891154 PMCID: PMC2377034 DOI: 10.1038/nature06216] [Citation(s) in RCA: 231] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2007] [Accepted: 09/04/2007] [Indexed: 02/07/2023]
Abstract
The retromer complex is required for the sorting of acid hydrolases to lysosomes, transcytosis of the polymeric immunoglobulin receptor, Wnt gradient formation, iron transporter recycling and processing of the amyloid precursor protein. Human retromer consists of two smaller complexes: the cargo recognition VPS26-VPS29-VPS35 heterotrimer and a membrane-targeting heterodimer or homodimer of SNX1 and/or SNX2 (ref. 13). Here we report the crystal structure of a VPS29-VPS35 subcomplex showing how the metallophosphoesterase-fold subunit VPS29 (refs 14, 15) acts as a scaffold for the carboxy-terminal half of VPS35. VPS35 forms a horseshoe-shaped, right-handed, alpha-helical solenoid, the concave face of which completely covers the metal-binding site of VPS29, whereas the convex face exposes a series of hydrophobic interhelical grooves. Electron microscopy shows that the intact VPS26-VPS29-VPS35 complex is a stick-shaped, flexible structure, approximately 21 nm long. A hybrid structural model derived from crystal structures, electron microscopy, interaction studies and bioinformatics shows that the alpha-solenoid fold extends the full length of VPS35, and that VPS26 is bound at the opposite end from VPS29. This extended structure presents multiple binding sites for the SNX complex and receptor cargo, and appears capable of flexing to conform to curved vesicular membranes.
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Affiliation(s)
- Aitor Hierro
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Adriana L. Rojas
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Raul Rojas
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Namita Murthy
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Grégory Effantin
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Andrey V. Kajava
- Centre de Recherches de Biochimie Macromoléculaire, CNRS, University of Montpellier, 1919 Route de Mende, 34293 Montpellier, France
| | - Alasdair C. Steven
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal, and Skin Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - Juan S. Bonifacino
- Cell Biology and Metabolism Branch, National Institute of Child Health and Human Development, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
| | - James H. Hurley
- Laboratory of Molecular Biology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, U. S. Department of Health and Human Services, Bethesda, MD 20892, USA
- To whom correspondence should be addressed:James H. Hurley, (301) 402−4703, fax (301) 480−0639; E-mail:
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405
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Iancu CV, Ding HJ, Morris DM, Dias DP, Gonzales AD, Martino A, Jensen GJ. The structure of isolated Synechococcus strain WH8102 carboxysomes as revealed by electron cryotomography. J Mol Biol 2007; 372:764-73. [PMID: 17669419 PMCID: PMC2453779 DOI: 10.1016/j.jmb.2007.06.059] [Citation(s) in RCA: 105] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2007] [Revised: 05/25/2007] [Accepted: 06/25/2007] [Indexed: 10/23/2022]
Abstract
Carboxysomes are organelle-like polyhedral bodies found in cyanobacteria and many chemoautotrophic bacteria that are thought to facilitate carbon fixation. Carboxysomes are bounded by a proteinaceous outer shell and filled with ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO), the first enzyme in the CO(2) fixation pathway, but exactly how they enhance carbon fixation is unclear. Here we report the three-dimensional structure of purified carboxysomes from Synechococcus species strain WH8102 as revealed by electron cryotomography. We found that while the sizes of individual carboxysomes in this organism varied from 114 nm to 137 nm, surprisingly, all were approximately icosahedral. There were on average approximately 250 RuBisCOs per carboxysome, organized into three to four concentric layers. Some models of carboxysome function depend on specific contacts between individual RuBisCOs and the shell, but no evidence of such contacts was found: no systematic patterns of connecting densities or RuBisCO positions against the shell's presumed hexagonal lattice could be discerned, and simulations showed that packing forces alone could account for the layered organization of RuBisCOs.
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Affiliation(s)
- Cristina V. Iancu
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - H. Jane Ding
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Dylan M. Morris
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - D. Prabha Dias
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
| | - Arlene D. Gonzales
- P.O. Box 5800, MS0895, Biomolecular Analysis and Imaging, Sandia National Laboratories, Alburquerque, NM 87195-0895, USA
| | - Anthony Martino
- P.O. Box 5800, MS0895, Biomolecular Analysis and Imaging, Sandia National Laboratories, Alburquerque, NM 87195-0895, USA
| | - Grant J. Jensen
- Division of Biology, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125, USA
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406
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Henderson GP, Gan L, Jensen GJ. 3-D ultrastructure of O. tauri: electron cryotomography of an entire eukaryotic cell. PLoS One 2007; 2:e749. [PMID: 17710148 PMCID: PMC1939878 DOI: 10.1371/journal.pone.0000749] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2007] [Accepted: 07/16/2007] [Indexed: 01/11/2023] Open
Abstract
The hallmark of eukaryotic cells is their segregation of key biological functions into discrete, membrane-bound organelles. Creating accurate models of their ultrastructural complexity has been difficult in part because of the limited resolution of light microscopy and the artifact-prone nature of conventional electron microscopy. Here we explored the potential of the emerging technology electron cryotomography to produce three-dimensional images of an entire eukaryotic cell in a near-native state. Ostreococcus tauri was chosen as the specimen because as a unicellular picoplankton with just one copy of each organelle, it is the smallest known eukaryote and was therefore likely to yield the highest resolution images. Whole cells were imaged at various stages of the cell cycle, yielding 3-D reconstructions of complete chloroplasts, mitochondria, endoplasmic reticula, Golgi bodies, peroxisomes, microtubules, and putative ribosome distributions in-situ. Surprisingly, the nucleus was seen to open long before mitosis, and while one microtubule (or two in some predivisional cells) was consistently present, no mitotic spindle was ever observed, prompting speculation that a single microtubule might be sufficient to segregate multiple chromosomes.
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Affiliation(s)
- Gregory P. Henderson
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Lu Gan
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
| | - Grant J. Jensen
- Division of Biology, California Institute of Technology, Pasadena, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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407
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Heymann JB, Cardone G, Winkler DC, Steven AC. Computational resources for cryo-electron tomography in Bsoft. J Struct Biol 2007; 161:232-42. [PMID: 17869539 PMCID: PMC2409064 DOI: 10.1016/j.jsb.2007.08.002] [Citation(s) in RCA: 124] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2007] [Revised: 07/30/2007] [Accepted: 08/01/2007] [Indexed: 11/21/2022]
Abstract
The Bsoft package [Heymann, J.B., Belnap, D.M., 2007. Bsoft: image processing and molecular modeling for electron microscopy. J. Struct. Biol. 157, 3-18] has been enhanced by adding utilities for processing electron tomographic (ET) data; in particular, cryo-ET data characterized by low contrast and high noise. To handle the high computational load efficiently, a workflow was developed, based on the database-like parameter handling in Bsoft, aimed at minimizing user interaction and facilitating automation. To the same end, scripting elements distribute the processing among multiple processors on the same or different computers. The resolution of a tomogram depends on the precision of projection alignment, which is usually based on pinpointing fiducial markers (electron-dense gold particles). Alignment requires accurate specification of the tilt axis, and our protocol includes a procedure for determining it to adequate accuracy. Refinement of projection alignment provides information that allows assessment of its precision, as well as projection quality control. We implemented a reciprocal space algorithm that affords an alternative to back-projection or real space algorithms for calculating tomograms. Resources are also included that allow resolution assessment by cross-validation (NLOO2D); denoising and interpretation; and the extraction, mutual alignment, and averaging of tomographic sub-volumes.
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Affiliation(s)
- J Bernard Heymann
- Laboratory of Structural Biology, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Building 50, Room 1515, 50 South Drive MSC 8025, Bethesda, MD 20892-8025, USA.
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408
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Trus BL, Newcomb WW, Cheng N, Cardone G, Marekov L, Homa FL, Brown JC, Steven AC. Allosteric signaling and a nuclear exit strategy: binding of UL25/UL17 heterodimers to DNA-Filled HSV-1 capsids. Mol Cell 2007; 26:479-89. [PMID: 17531807 PMCID: PMC1945812 DOI: 10.1016/j.molcel.2007.04.010] [Citation(s) in RCA: 123] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2007] [Revised: 03/16/2007] [Accepted: 04/10/2007] [Indexed: 10/23/2022]
Abstract
UL25 and UL17 are two essential minor capsid proteins of HSV-1, implicated in DNA packaging and capsid maturation. We used cryo-electron microscopy to examine their binding to capsids, whose architecture observes T = 16 icosahedral geometry. C-capsids (mature DNA-filled capsids) have an elongated two-domain molecule present at a unique, vertex-adjacent site that is not seen at other quasiequivalent sites or on unfilled capsids. Using SDS-PAGE and mass spectrometry to analyze wild-type capsids, UL25 null capsids, and denaturant-extracted capsids, we conclude that (1) the C-capsid-specific component is a heterodimer of UL25 and UL17, and (2) capsids have additional populations of UL25 and UL17 that are invisible in reconstructions because of sparsity and/or disorder. We infer that binding of the ordered population reflects structural changes induced on the outer surface as pressure builds up inside the capsid during DNA packaging. Its binding may signal that the C-capsid is ready to exit the nucleus.
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Affiliation(s)
- Benes L. Trus
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- Imaging Sciences Laboratory, Division of Computational Bioscience, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - William W. Newcomb
- Department of Microbiology and Cancer Center, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Giovanni Cardone
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Lyuben Marekov
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Fred L. Homa
- Department of Molecular Genetics and Biochemistry, University of Pittsburgh School of Medicine, Pittsburgh, PA 15261, USA
| | - Jay C. Brown
- Department of Microbiology and Cancer Center, University of Virginia Health System, Charlottesville, VA 22908, USA
| | - Alasdair C. Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892, USA
- * Correspondence: Building 50, Rm 1517, MSC 8025, 50 South Drive, National Institutes of Health, Bethesda, MD 20892-8025 U.S.A., tel: 301 496 0132; fax 301 443 7651,
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409
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Salvi E, Cantele F, Zampighi L, Fain N, Pigino G, Zampighi G, Lanzavecchia S. JUST (Java User Segmentation Tool) for semi-automatic segmentation of tomographic maps. J Struct Biol 2007; 161:287-97. [PMID: 17707657 PMCID: PMC2692284 DOI: 10.1016/j.jsb.2007.06.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2007] [Revised: 05/16/2007] [Accepted: 06/21/2007] [Indexed: 10/23/2022]
Abstract
We are presenting a program for interactive segmentation of tomographic maps, based on objective criteria so as to yield reproducible results. The strategy starts with the automatic segmentation of the entire volume with the watershed algorithm in 3D. The watershed regions are clustered successively by supervised classification, allowing the segmentation of known organelles, such as membranes, vesicles and microtubules. These organelles are processed with topological models and input parameters manually derived from the tomograms. After known organelles are extracted from the volume, all other watershed regions can be organized into homogeneous assemblies on the basis of their densities. To complete the process, all voxels in the volume are assigned either to the background or individual structures, which can then be extracted for visualization with any rendering technique. The user interface of the program is written in Java, and computational routines are written in C. For some operations, involving the visualization of the tomogram, we refer to existing software, either open or commercial. While the program runs, a history file is created, that allows all parameters and other data to be saved for the purposes of comparison or exchange. Initially, the program was developed for the segmentation of synapses, and organelles belonging to these structures have thus far been the principal targets modeled with JUST. Since each organelle is clustered independently from the rest of the volume, however, the program can accommodate new models of different organelles as well as tomograms of other types of preparations of tissue, such as cytoskeletal components in vitreous ice.
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Affiliation(s)
- Eleonora Salvi
- Department of Structural Chemistry, School of Pharmacy, University of Milan, Italy
| | - Francesca Cantele
- Department of Structural Chemistry, School of Pharmacy, University of Milan, Italy
| | - Lorenzo Zampighi
- Department Physiology, UCLA School of Medicine, Los Angeles, California
| | - Nick Fain
- Department Neurobiology, UCLA School of Medicine, Los Angeles, California
| | - Gaia Pigino
- Department of Evolutionary Biology, University of Siena, Italy
| | - Guido Zampighi
- Department Neurobiology, UCLA School of Medicine, Los Angeles, California
- Department Jules Stein Eye Research Institute, UCLA School of Medicine, Los Angeles, California
| | - Salvatore Lanzavecchia
- Department of Structural Chemistry, School of Pharmacy, University of Milan, Italy
- Author for Correspondence: Salvatore Lanzavecchia, University of Milano, Dept. of Structural Chemistry, Via G. Venezian 21, 20133, Milano, Italy, Tel: (+39) 02 5031 4444, Fax: (+39) 02 5031 4454, e-mail:
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410
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Sorzano COS, Jonic S, Cottevieille M, Larquet E, Boisset N, Marco S. 3D electron microscopy of biological nanomachines: principles and applications. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:995-1013. [PMID: 17611751 DOI: 10.1007/s00249-007-0203-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2007] [Revised: 06/01/2007] [Accepted: 06/11/2007] [Indexed: 11/21/2022]
Abstract
Transmission electron microscopy is a powerful technique for studying the three-dimensional (3D) structure of a wide range of biological specimens. Knowledge of this structure is crucial for fully understanding complex relationships among macromolecular complexes and organelles in living cells. In this paper, we present the principles and main application domains of 3D transmission electron microscopy in structural biology. Moreover, we survey current developments needed in this field, and discuss the close relationship of 3D transmission electron microscopy with other experimental techniques aimed at obtaining structural and dynamical information from the scale of whole living cells to atomic structure of macromolecular complexes.
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Affiliation(s)
- C O S Sorzano
- Bioengineering Lab, Escuela Politécnica Superior, Univ. San Pablo CEU, Campus Urb, Montepríncipe s/n, 28668, Boadilla del Monte, Madrid, Spain.
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411
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Sabaté R, Baxa U, Benkemoun L, Sánchez de Groot N, Coulary-Salin B, Maddelein ML, Malato L, Ventura S, Steven AC, Saupe SJ. Prion and Non-prion Amyloids of the HET-s Prion forming Domain. J Mol Biol 2007; 370:768-83. [PMID: 17532341 DOI: 10.1016/j.jmb.2007.05.014] [Citation(s) in RCA: 60] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2007] [Revised: 04/23/2007] [Accepted: 05/05/2007] [Indexed: 11/19/2022]
Abstract
HET-s is a prion protein of the fungus Podospora anserina. A plausible structural model for the infectious amyloid fold of the HET-s prion-forming domain, HET-s(218-289), makes it an attractive system to study structure-function relationships in amyloid assembly and prion propagation. Here, we report on the diversity of HET-s(218-289) amyloids formed in vitro. We distinguish two types formed at pH 7 from fibrils formed at pH 2, on morphological grounds. Unlike pH 7 fibrils, the pH 2 fibrils show very little if any prion infectivity. They also differ in ThT-binding, resistance to denaturants, assembly kinetics, secondary structure, and intrinsic fluorescence. Both contain 5 nm fibrils, either bundled or disordered (pH 7) or as tightly twisted protofibrils (pH 2). We show that electrostatic interactions are critical for the formation and stability of the infectious prion fold given in the current model. The altered properties of the amyloid assembled at pH 2 may arise from a perturbation in the subunit fold or fibrillar stacking.
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Affiliation(s)
- Raimon Sabaté
- Laboratoire de Génétique Moléculaire des Champignons, Institut de Biochimie et de Génétique Cellulaires,UMR 5095 CNRS/Université de Bordeaux 2, 1 rue Camille St Saëns, 33077 Bordeaux cedex, France
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412
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Jensen GJ, Briegel A. How electron cryotomography is opening a new window onto prokaryotic ultrastructure. Curr Opin Struct Biol 2007; 17:260-7. [PMID: 17398087 DOI: 10.1016/j.sbi.2007.03.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2006] [Revised: 02/13/2007] [Accepted: 03/12/2007] [Indexed: 11/22/2022]
Abstract
Electron cryotomography is an emerging technology that enables thin samples, including small intact prokaryotic cells, to be imaged in three dimensions in a near-native 'frozen-hydrated' state to a resolution sufficient to recognize very large macromolecular complexes in situ. Following years of visionary technology development by a few key pioneers, several laboratories are now using the technique to produce biological results of major significance in the field of prokaryotic ultrastructure. Recent discoveries have included the surprising generality and complexity of the cytoskeleton, the connectivity of key membrane compartments, the location and architecture of large macromolecular machines such as the ribosome and flagellar motors, and the structure of some extraordinary external appendages. Through further technology development, identification of the most revealing model systems and sustained effort, electron cryotomography is poised to help resolve many fundamentally important questions about prokaryotic ultrastructure.
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Affiliation(s)
- Grant J Jensen
- Division of Biology, California Institute of Technology, Pasadena, CA 91125, USA.
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413
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Cardone G, Winkler DC, Trus BL, Cheng N, Heuser JE, Newcomb WW, Brown JC, Steven AC. Visualization of the herpes simplex virus portal in situ by cryo-electron tomography. Virology 2006; 361:426-34. [PMID: 17188319 PMCID: PMC1930166 DOI: 10.1016/j.virol.2006.10.047] [Citation(s) in RCA: 98] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2006] [Revised: 10/17/2006] [Accepted: 10/27/2006] [Indexed: 11/18/2022]
Abstract
Herpes simplex virus type 1 (HSV-1), the prototypical herpesvirus, has an icosahedral nucleocapsid surrounded by a proteinaceous tegument and a lipoprotein envelope. As in tailed bacteriophages, the icosahedral symmetry of the capsid is broken at one of the 12 vertices, which is occupied by a dodecameric ring of portal protein, UL6, instead of a pentamer of the capsid protein, UL19. The portal ring serves as a conduit for DNA entering and exiting the capsid. From a cryo-EM reconstruction of capsids immuno-gold-labeled with anti-UL6 antibodies, we confirmed that UL6 resides at a vertex. To visualize the portal in the context of the assembled capsid, we used cryo-electron tomography to determine the three-dimensional structures of individual A-capsids (empty, mature capsids). The similarity in size and overall shape of the portal and a UL19 pentamer--both are cylinders of approximately 800 kDa--combined with residual noise in the tomograms, prevented us from identifying the portal vertices directly; however, this was accomplished by a computational classification procedure. Averaging the portal-containing subtomograms produced a structure that tallies with the isolated portal, as previously reconstructed by cryo-EM. The portal is mounted on the outer surface of the capsid floor layer, with its narrow end pointing outwards. This disposition differs from that of known phage portals in that the bulk of its mass lies outside, not inside, the floor. This distinction may be indicative of divergence at the level of portal-related functions other than its role as a DNA channel.
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Affiliation(s)
- Giovanni Cardone
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892
| | - Dennis C. Winkler
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892
| | - Benes L. Trus
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892
- Imaging Sciences Laboratory, Division of Computational Bioscience, Center for Information Technology; National Institutes of Health, Bethesda, MD 20892
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892
| | - John E. Heuser
- Department of Cell Biology, Washington University School of Medicine, St. Louis, MO 63110
| | - William W. Newcomb
- Department of Microbiology and Cancer Center, University of Virginia Health System, Charlottesville, VA 22908
| | - Jay C. Brown
- Department of Microbiology and Cancer Center, University of Virginia Health System, Charlottesville, VA 22908
| | - Alasdair C. Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, Bethesda, MD 20892
- * Correspondence : Building 50, Rm 1517, MSC 8025, 50 South Drive, National Institutes of Health, Bethesda MD 20892-8025, tel: 301 496 0132; fax 301 443 7651;
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van der Heide P, Xu XP, Marsh BJ, Hanein D, Volkmann N. Efficient automatic noise reduction of electron tomographic reconstructions based on iterative median filtering. J Struct Biol 2006; 158:196-204. [PMID: 17224280 DOI: 10.1016/j.jsb.2006.10.030] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2006] [Revised: 10/20/2006] [Accepted: 10/23/2006] [Indexed: 10/23/2022]
Abstract
A simple, fast and efficient noise-reduction protocol for three-dimensional electron tomographic reconstructions of biological material is presented. The approach is based on iterative application of median filtering and shows promise for automatic noise reduction as a pre-processor for automated data analysis tools which aim at segmentation, feature extraction and pattern recognition. The application of this algorithm produces encouraging results for a wide variety of experimental and synthetic electron tomographic reconstructions.
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