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Xue H, Zhang M, Liu J, Wang J, Ren G. Cryo-electron tomography related radiation-damage parameters for individual-molecule 3D structure determination. Front Chem 2022; 10:889203. [PMID: 36110139 PMCID: PMC9468540 DOI: 10.3389/fchem.2022.889203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Accepted: 07/13/2022] [Indexed: 11/28/2022] Open
Abstract
To understand the dynamic structure-function relationship of soft- and biomolecules, the determination of the three-dimensional (3D) structure of each individual molecule (nonaveraged structure) in its native state is sought-after. Cryo-electron tomography (cryo-ET) is a unique tool for imaging an individual object from a series of tilted views. However, due to radiation damage from the incident electron beam, the tolerable electron dose limits image contrast and the signal-to-noise ratio (SNR) of the data, preventing the 3D structure determination of individual molecules, especially at high-resolution. Although recently developed technologies and techniques, such as the direct electron detector, phase plate, and computational algorithms, can partially improve image contrast/SNR at the same electron dose, the high-resolution structure, such as tertiary structure of individual molecules, has not yet been resolved. Here, we review the cryo-electron microscopy (cryo-EM) and cryo-ET experimental parameters to discuss how these parameters affect the extent of radiation damage. This discussion can guide us in optimizing the experimental strategy to increase the imaging dose or improve image SNR without increasing the radiation damage. With a higher dose, a higher image contrast/SNR can be achieved, which is crucial for individual-molecule 3D structure. With 3D structures determined from an ensemble of individual molecules in different conformations, the molecular mechanism through their biochemical reactions, such as self-folding or synthesis, can be elucidated in a straightforward manner.
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Affiliation(s)
- Han Xue
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Meng Zhang
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianfang Liu
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
| | - Jianjun Wang
- Beijing National Laboratory for Molecular Science, Institute of Chemistry, Chinese Academy of Sciences, Beijing, China
| | - Gang Ren
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, United States
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Villalta A, Schmitt A, Estrozi LF, Quemin ERJ, Alempic JM, Lartigue A, Pražák V, Belmudes L, Vasishtan D, Colmant AMG, Honoré FA, Couté Y, Grünewald K, Abergel C. The giant mimivirus 1.2 Mb genome is elegantly organized into a 30-nm diameter helical protein shield. eLife 2022; 11:e77607. [PMID: 35900198 PMCID: PMC9512402 DOI: 10.7554/elife.77607] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 07/27/2022] [Indexed: 11/13/2022] Open
Abstract
Mimivirus is the prototype of the Mimiviridae family of giant dsDNA viruses. Little is known about the organization of the 1.2 Mb genome inside the membrane-limited nucleoid filling the ~0.5 µm icosahedral capsids. Cryo-electron microscopy, cryo-electron tomography, and proteomics revealed that it is encased into a ~30-nm diameter helical protein shell surprisingly composed of two GMC-type oxidoreductases, which also form the glycosylated fibrils decorating the capsid. The genome is arranged in 5- or 6-start left-handed super-helices, with each DNA-strand lining the central channel. This luminal channel of the nucleoprotein fiber is wide enough to accommodate oxidative stress proteins and RNA polymerase subunits identified by proteomics. Such elegant supramolecular organization would represent a remarkable evolutionary strategy for packaging and protecting the genome, in a state ready for immediate transcription upon unwinding in the host cytoplasm. The parsimonious use of the same protein in two unrelated substructures of the virion is unexpected for a giant virus with thousand genes at its disposal.
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Affiliation(s)
- Alejandro Villalta
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Alain Schmitt
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Leandro F Estrozi
- Univ. Grenoble Alpes, CNRS, CEA, Institut de Biologie Structurale (IBS)GrenobleFrance
| | - Emmanuelle RJ Quemin
- Centre for Structural Systems Biology, Leibniz Institute for Experimental Virology (HPI), University of HamburgHamburgGermany
| | - Jean-Marie Alempic
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Audrey Lartigue
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Vojtěch Pražák
- Centre for Structural Systems Biology, Leibniz Institute for Experimental Virology (HPI), University of HamburgHamburgGermany
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Lucid Belmudes
- Univ. Grenoble Alpes, CEA, INSERM, IRIG, BGEGrenobleFrance
| | - Daven Vasishtan
- Centre for Structural Systems Biology, Leibniz Institute for Experimental Virology (HPI), University of HamburgHamburgGermany
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Agathe MG Colmant
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Flora A Honoré
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
| | - Yohann Couté
- Univ. Grenoble Alpes, CEA, INSERM, IRIG, BGEGrenobleFrance
| | - Kay Grünewald
- Centre for Structural Systems Biology, Leibniz Institute for Experimental Virology (HPI), University of HamburgHamburgGermany
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of OxfordOxfordUnited Kingdom
| | - Chantal Abergel
- Aix–Marseille University, Centre National de la Recherche Scientifique, Information Génomique & Structurale, Unité Mixte de Recherche 7256 (Institut de Microbiologie de la Méditerranée, FR3479, IM2B)MarseilleFrance
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Swanson NA, Hou CFD, Cingolani G. Viral Ejection Proteins: Mosaically Conserved, Conformational Gymnasts. Microorganisms 2022; 10:microorganisms10030504. [PMID: 35336080 PMCID: PMC8954989 DOI: 10.3390/microorganisms10030504] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Revised: 02/18/2022] [Accepted: 02/22/2022] [Indexed: 11/16/2022] Open
Abstract
Bacterial viruses (or bacteriophages) have developed formidable ways to deliver their genetic information inside bacteria, overcoming the complexity of the bacterial-cell envelope. In short-tailed phages of the Podoviridae superfamily, genome ejection is mediated by a set of mysterious internal virion proteins, also called ejection or pilot proteins, which are required for infectivity. The ejection proteins are challenging to study due to their plastic structures and transient assembly and have remained less characterized than classical components such as the phage coat protein or terminase subunit. However, a spate of recent cryo-EM structures has elucidated key features underscoring these proteins' assembly and conformational gymnastics that accompany their expulsion from the virion head through the portal protein channel into the host. In this review, we will use a phage-T7-centric approach to critically review the status of the literature on ejection proteins, decipher the conformational changes of T7 ejection proteins in the pre- and post-ejection conformation, and predict the conservation of these proteins in other Podoviridae. The challenge is to relate the structure of the ejection proteins to the mechanisms of genome ejection, which are exceedingly complex and use the host's machinery.
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Affiliation(s)
- Nicholas A. Swanson
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; (N.A.S.); (C.-F.D.H.)
- Department of Biology, Massachusetts Institute of Technology, 31 Ames Street, Cambridge, MA 02139, USA
| | - Chun-Feng D. Hou
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; (N.A.S.); (C.-F.D.H.)
| | - Gino Cingolani
- Department of Biochemistry and Molecular Biology, Thomas Jefferson University, 1020 Locust Street, Philadelphia, PA 19107, USA; (N.A.S.); (C.-F.D.H.)
- Correspondence: ; Tel.: +01-(215)-503-4573
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Wu W, Cheng N, Black LW, Dietz H, Steven AC. Biphasic Packing of DNA and Internal Proteins in Bacteriophage T4 Heads Revealed by Bubblegram Imaging. Viruses 2020; 12:v12111282. [PMID: 33182609 PMCID: PMC7697877 DOI: 10.3390/v12111282] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Revised: 11/03/2020] [Accepted: 11/04/2020] [Indexed: 11/17/2022] Open
Abstract
The virions of tailed bacteriophages and the evolutionarily related herpesviruses contain, in addition to highly condensed DNA, substantial quantities of internal proteins. These proteins (“ejection proteins”) have roles in scaffolding, maturational proteolysis, and cell-to-cell delivery. Whereas capsids are amenable to analysis at high resolution by cryo-electron microscopy, internal proteins have proved difficult to localize. In this study, we investigated the distribution of internal proteins in T4 by bubblegram imaging. Prior work has shown that at suitably high electron doses, radiation damage generates bubbles of hydrogen gas in nucleoprotein specimens. Using DNA origami as a test specimen, we show that DNA does not bubble under these conditions; it follows that bubbles represent markers for proteins. The interior of the prolate T4 head, ~1000 Å long by ~750 Å wide, has a bubble-free zone that is ~100–110 Å thick, underlying the capsid shell from which proteins are excluded by highly ordered DNA. Inside this zone, which is plausibly occupied by ~4 layers of coaxial spool, bubbles are generated at random locations in a disordered ensemble of internal proteins and the remainder of the genome.
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Affiliation(s)
- Weimin Wu
- Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-8025, USA;
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-8025, USA;
| | - Lindsay W. Black
- Department of Biochemistry and Molecular Biology, University of Maryland Medical School, Baltimore, MD 21201-1503, USA;
| | - Hendrik Dietz
- Physics Department, Technische Universität München, 85748 Garching-bei-München, Germany;
| | - Alasdair C. Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD 20892-8025, USA;
- Correspondence: ; Tel.: +1-(301)-496-0132; Fax: +1-(301)-443-7651
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Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy. Viruses 2018; 10:v10020067. [PMID: 29414851 PMCID: PMC5850374 DOI: 10.3390/v10020067] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 01/26/2018] [Accepted: 01/31/2018] [Indexed: 12/19/2022] Open
Abstract
The majority of viruses on Earth form capsids built by multiple copies of one or more types of a coat protein arranged with 532 symmetry, generating an icosahedral shell. This highly repetitive structure is ideal to closely pack identical protein subunits and to enclose the nucleic acid genomes. However, the icosahedral capsid is not merely a passive cage but undergoes dynamic events to promote packaging, maturation and the transfer of the viral genome into the host. These essential processes are often mediated by proteinaceous complexes that interrupt the shell’s icosahedral symmetry, providing a gateway through the capsid. In this review, we take an inventory of molecular structures observed either internally, or at the 5-fold vertices of icosahedral DNA viruses that infect bacteria, archea and eukaryotes. Taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of individual components, we review the design principles of non-icosahedral structural components that interrupt icosahedral symmetry and discuss how these macromolecules play vital roles in genome packaging, ejection and host receptor-binding.
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Abstract
Tailed bacteriophages with genomes larger than 200 kbp are classified as Jumbo phages, and are rarely isolated by conventional methods. These phages are designated “jumbo” owing to their most notable features of a large phage virion and large genome size. However, in addition to these, jumbo phages also exhibit several novel characteristics that have not been observed for phages with smaller genomes, which differentiate jumbo phages in terms of genome organization, virion structure, progeny propagation, and evolution. In this review, we summarize available reports on jumbo phages and discuss the differences between jumbo phages and small-genome phages. We also discuss data suggesting that jumbo phages might have evolved from phages with smaller genomes by acquiring additional functional genes, and that these additional genes reduce the dependence of the jumbo phages on the host bacteria.
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Affiliation(s)
- Yihui Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, PR, China
| | - Meiying Gao
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences Wuhan, PR, China
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Mishyna M, Volokh O, Danilova Y, Gerasimova N, Pechnikova E, Sokolova OS. Effects of radiation damage in studies of protein-DNA complexes by cryo-EM. Micron 2017; 96:57-64. [PMID: 28262565 DOI: 10.1016/j.micron.2017.02.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2016] [Revised: 02/18/2017] [Accepted: 02/18/2017] [Indexed: 11/26/2022]
Abstract
Nucleic acids are responsible for the storage, transfer and realization of genetic information in the cell, which provides correct development and functioning of organisms. DNA interaction with ligands ensures the safety of this information. Over the past 10 years, advances in electron microscopy and image processing allowed to obtain the structures of key DNA-protein complexes with resolution below 4Å. However, radiation damage is a limiting factor to the potentially attainable resolution in cryo-EM. The prospect and limitations of studying protein-DNA complex interactions using cryo-electron microscopy are discussed here. We reviewed the ways to minimize radiation damage in biological specimens and the possibilities of using radiation damage (so-called 'bubblegrams') to obtain additional structural information.
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Affiliation(s)
- M Mishyna
- Lomonosov Moscow State University, 119234, Moscow, Russia.
| | - O Volokh
- Lomonosov Moscow State University, 119234, Moscow, Russia
| | - Ya Danilova
- Lomonosov Moscow State University, 119234, Moscow, Russia
| | - N Gerasimova
- Lomonosov Moscow State University, 119234, Moscow, Russia
| | - E Pechnikova
- Thermo Fisher Scientific, Materials & Structural Analysis, 5651 GG Eindhoven, Netherlands
| | - O S Sokolova
- Lomonosov Moscow State University, 119234, Moscow, Russia.
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8
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Localization of the Houdinisome (Ejection Proteins) inside the Bacteriophage P22 Virion by Bubblegram Imaging. mBio 2016; 7:mBio.01152-16. [PMID: 27507825 PMCID: PMC4992974 DOI: 10.1128/mbio.01152-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The P22 capsid is a T=7 icosahedrally symmetric protein shell with a portal protein dodecamer at one 5-fold vertex. Extending outwards from that vertex is a short tail, and putatively extending inwards is a 15-nm-long α-helical barrel formed by the C-terminal domains of portal protein subunits. In addition to the densely packed genome, the capsid contains three “ejection proteins” (E-proteins [gp7, gp16, and gp20]) destined to exit from the tightly sealed capsid during the process of DNA delivery into target cells. We estimated their copy numbers by quantitative SDS-PAGE as approximately 12 molecules per virion of gp16 and gp7 and 30 copies of gp20. To localize them, we used bubblegram imaging, an adaptation of cryo-electron microscopy in which gaseous bubbles induced in proteins by prolonged irradiation are used to map the proteins’ locations. We applied this technique to wild-type P22, a triple mutant lacking all three E-proteins, and three mutants each lacking one E-protein. We conclude that all three E-proteins are loosely clustered around the portal axis, in the region displaced radially inwards from the portal crown. The bubblegram data imply that approximately half of the α-helical barrel seen in the portal crystal structure is disordered in the mature virion, and parts of the disordered region present binding sites for E-proteins. Thus positioned, the E-proteins are strategically placed to pass down the shortened barrel and through the portal ring and the tail, as they exit from the capsid during an infection. While it has long been appreciated that capsids serve as delivery vehicles for viral genomes, there is now growing awareness that viruses also deliver proteins into their host cells. P22 has three such proteins (ejection proteins [E-proteins]), whose initial locations in the virion have remained unknown despite their copious amounts (total of 2.5 MDa). This study succeeded in localizing them by the novel technique of bubblegram imaging. The P22 E-proteins are seen to be distributed around the orifice of the portal barrel. Interestingly, this barrel, 15 nm long in a crystal structure, is only about half as long in situ: the remaining, disordered, portion appears to present binding sites for E-proteins. These observations document a spectacular example of a regulatory order-disorder transition in a supramolecular system and demonstrate the potential of bubblegram imaging to map the components of other viruses as well as cellular complexes.
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Abstract
It has long been known that cryo-EM specimens are severely damaged by a level of electron exposure that is much lower than what is needed to obtain high-resolution images from single macromolecules. Perhaps less well appreciated in the cryo-EM literature, the vitreous ice in which samples are suspended is equally sensitivity to radiation damage. This chapter provides a review of several fundamental topics such as inelastic scattering of electrons, radiation chemistry, and radiation biology, which-together-can help one to understand why radiation damage occurs so "easily." This chapter also addresses the issue of beam-induced motion that occurs at even lower levels of electron exposure. While specimen charging may be a contributor to this motion, it is argued that both radiation-induced relief of preexisting stress and damage-induced generation of additional stress may be the dominant causes of radiation-induced movement.
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Affiliation(s)
- R M Glaeser
- Lawrence Berkeley National Laboratory, University of California, Berkeley, CA, United States.
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Wu W, Newcomb WW, Cheng N, Aksyuk A, Winkler DC, Steven AC. Internal Proteins of the Procapsid and Mature Capsids of Herpes Simplex Virus 1 Mapped by Bubblegram Imaging. J Virol 2016; 90:5176-86. [PMID: 26984725 PMCID: PMC4859710 DOI: 10.1128/jvi.03224-15] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2015] [Accepted: 03/09/2016] [Indexed: 02/08/2023] Open
Abstract
UNLABELLED The herpes simplex virus 1 (HSV-1) capsid is a huge assembly, ∼1,250 Å in diameter, and is composed of thousands of protein subunits with a combined mass of ∼200 MDa, housing a 100-MDa genome. First, a procapsid is formed through coassembly of the surface shell with an inner scaffolding shell; then the procapsid matures via a major structural transformation, triggered by limited proteolysis of the scaffolding proteins. Three mature capsids are found in the nuclei of infected cells. A capsids are empty, B capsids retain a shrunken scaffolding shell, and C capsids-which develop into infectious virions-are filled with DNA and ostensibly have expelled the scaffolding shell. The possible presence of other internal proteins in C capsids has been moot as, in cryo-electron microscopy (cryo-EM), they would be camouflaged by the surrounding DNA. We have used bubblegram imaging to map internal proteins in all four capsids, aided by the discovery that the scaffolding protein is exceptionally prone to radiation-induced bubbling. We confirmed that this protein forms thick-walled inner shells in the procapsid and the B capsid. C capsids generate two classes of bubbles: one occupies positions beneath the vertices of the icosahedral surface shell, and the other is distributed throughout its interior. A likely candidate is the viral protease. A subpopulation of C capsids bubbles particularly profusely and may represent particles in which expulsion of scaffold and DNA packaging are incomplete. Based on the procapsid structure, we propose that the axial channels of hexameric capsomers afford the pathway via which the scaffolding protein is expelled. IMPORTANCE In addition to DNA, capsids of tailed bacteriophages and their distant relatives, herpesviruses, contain internal proteins. These proteins are often essential for infectivity but are difficult to locate within the virion. A novel adaptation of cryo-EM based on detecting gas bubbles generated by radiation damage was used to localize internal proteins of HSV-1, yielding insights into how capsid maturation is regulated. The scaffolding protein, which forms inner shells in the procapsid and B capsid, is exceptionally bubbling-prone. In the mature DNA-filled C capsid, a previously undetected protein was found to underlie the icosahedral vertices: this is tentatively assigned as a storage form of the viral protease. We also observed a capsid species that appears to contain substantial amounts of scaffolding protein as well as DNA, suggesting that DNA packaging and expulsion of the scaffolding protein are coupled processes.
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Affiliation(s)
- Weimin Wu
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - William W Newcomb
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Anastasia Aksyuk
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Dennis C Winkler
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Nascimento TL, Hillaireau H, Noiray M, Bourgaux C, Arpicco S, Pehau-Arnaudet G, Taverna M, Cosco D, Tsapis N, Fattal E. Supramolecular Organization and siRNA Binding of Hyaluronic Acid-Coated Lipoplexes for Targeted Delivery to the CD44 Receptor. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:11186-11194. [PMID: 26375384 DOI: 10.1021/acs.langmuir.5b01979] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The dynamics of the formation of siRNA-lipoplexes coated with hyaluronic acid (HA) and the parameters influencing their supramolecular organization were studied. The insertion of a HA-dioleylphosphatidylethanolamine (DOPE) conjugate in the liposome structure as well as subsequent complexation with siRNA increased the liposome size. Lipoplexes were around 110 nm at high ± charge ratios with a zeta potential around +50 mV and around 230 nm at low ± ratios, with a zeta potential that decreased to negative values, reaching -45 mV. The addition of the conjugate did not compromise siRNA binding to liposomes, although these nucleic acids induced a displacement of part of the HA-DOPE conjugate upon lipoplex formation, as confirmed by capillary electrophoresis. Isothermal titration calorimetry, X-ray diffraction studies, and cryo-TEM microscopy demonstrated that in addition to electrostatic interactions with siRNA a rearrangement of the lipid bilayers takes place, resulting in condensed oligolamellar vesicles. This phenomenon is dependent on the number of siRNA molecules and the degree of modification with HA. Finally, the suitable positioning of HA on the lipoplex surface and its ability to bind specifically to the CD44 receptors in a concentration-dependent manner was demonstrated by surface plasmon resonance analysis.
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Affiliation(s)
- Thais L Nascimento
- Faculté de Pharmacie, Institut Galien Paris-Sud. Université Paris-Sud , LabEx LERMIT, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
- CNRS, UMR 8612, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
- CAPES Foundation, Ministry of Education of Brazil, Brasília DF 70040-020, Brazil
| | - Hervé Hillaireau
- Faculté de Pharmacie, Institut Galien Paris-Sud. Université Paris-Sud , LabEx LERMIT, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
- CNRS, UMR 8612, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
| | - Magali Noiray
- Faculté de Pharmacie, Institut Galien Paris-Sud. Université Paris-Sud , LabEx LERMIT, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
- CNRS, UMR 8612, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
| | - Claudie Bourgaux
- Faculté de Pharmacie, Institut Galien Paris-Sud. Université Paris-Sud , LabEx LERMIT, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
- CNRS, UMR 8612, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
| | - Silvia Arpicco
- Dipartemento di Scienza e Tecnologia del Farmaco, Università degli Studi di Torino, Facoltà di Farmacia , Via Pietro Giuria 9, 10125 Torino, Italy
| | - Gérard Pehau-Arnaudet
- Institut Pasteur, Plate-Forme de Microscopie Ultrastructurale, 25-28 rue du Docteur Roux, 75015 Paris, France
| | - Myriam Taverna
- Faculté de Pharmacie, Institut Galien Paris-Sud. Université Paris-Sud , LabEx LERMIT, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
- CNRS, UMR 8612, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
| | - Donato Cosco
- Department of Health Sciences, University "Magna Græcia" of Catanzaro, Campus Universitario "S. Venuta" , Viale S. Venuta, Germaneto, I-88100 Catanzaro, Italy
| | - Nicolas Tsapis
- Faculté de Pharmacie, Institut Galien Paris-Sud. Université Paris-Sud , LabEx LERMIT, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
- CNRS, UMR 8612, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
| | - Elias Fattal
- Faculté de Pharmacie, Institut Galien Paris-Sud. Université Paris-Sud , LabEx LERMIT, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
- CNRS, UMR 8612, 5 rue JB Clément, 92296 Châtenay-Malabry Cedex, France
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Fontana J, Jurado KA, Cheng N, Ly NL, Fuchs JR, Gorelick RJ, Engelman AN, Steven AC. Distribution and Redistribution of HIV-1 Nucleocapsid Protein in Immature, Mature, and Integrase-Inhibited Virions: a Role for Integrase in Maturation. J Virol 2015; 89:9765-80. [PMID: 26178982 PMCID: PMC4577894 DOI: 10.1128/jvi.01522-15] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2015] [Accepted: 07/09/2015] [Indexed: 12/24/2022] Open
Abstract
UNLABELLED During virion maturation, HIV-1 capsid protein assembles into a conical core containing the viral ribonucleoprotein (vRNP) complex, thought to be composed mainly of the viral RNA and nucleocapsid protein (NC). After infection, the viral RNA is reverse transcribed into double-stranded DNA, which is then incorporated into host chromosomes by integrase (IN) catalysis. Certain IN mutations (class II) and antiviral drugs (allosteric IN inhibitors [ALLINIs]) adversely affect maturation, resulting in virions that contain "eccentric condensates," electron-dense aggregates located outside seemingly empty capsids. Here we demonstrate that in addition to this mislocalization of electron density, a class II IN mutation and ALLINIs each increase the fraction of virions with malformed capsids (from ∼ 12% to ∼ 53%). Eccentric condensates have a high NC content, as demonstrated by "tomo-bubblegram" imaging, a novel labeling technique that exploits the susceptibility of NC to radiation damage. Tomo-bubblegrams also localized NC inside wild-type cores and lining the spherical Gag shell in immature virions. We conclude that eccentric condensates represent nonpackaged vRNPs and that either genetic or pharmacological inhibition of IN can impair vRNP incorporation into mature cores. Supplying IN in trans as part of a Vpr-IN fusion protein partially restored the formation of conical cores with internal electron density and the infectivity of a class II IN deletion mutant virus. Moreover, the ability of ALLINIs to induce eccentric condensate formation required both IN and viral RNA. Based on these observations, we propose a role for IN in initiating core morphogenesis and vRNP incorporation into the mature core during HIV-1 maturation. IMPORTANCE Maturation, a process essential for HIV-1 infectivity, involves core assembly, whereby the viral ribonucleoprotein (vRNP, composed of vRNA and nucleocapsid protein [NC]) is packaged into a conical capsid. Allosteric integrase inhibitors (ALLINIs) affect multiple viral processes. We have characterized ALLINIs and integrase mutants that have the same phenotype. First, by comparing the effects of ALLINIs on several steps of the viral cycle, we show that inhibition of maturation accounts for compound potency. Second, by using cryoelectron tomography, we find that ALLINIs impair conical capsid assembly. Third, by developing tomo-bubblegram imaging, which specifically labels NC protein, we find that ALLINIs block vRNP packaging; instead, vRNPs form "eccentric condensates" outside the core. Fourth, malformed cores, typical of integrase-deleted virus, are partially replaced by conical cores when integrase is supplied in trans. Fifth, vRNA is necessary for ALLINI-induced eccentric condensate formation. These observations suggest that integrase is involved in capsid morphogenesis and vRNP packaging.
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Affiliation(s)
- Juan Fontana
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Kellie A Jurado
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Naiqian Cheng
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Ngoc L Ly
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - James R Fuchs
- Division of Medicinal Chemistry and Pharmacognosy, College of Pharmacy, The Ohio State University, Columbus, Ohio, USA
| | - Robert J Gorelick
- AIDS and Cancer Virus Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - Alan N Engelman
- Department of Cancer Immunology and AIDS, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Alasdair C Steven
- Laboratory of Structural Biology Research, National Institute of Arthritis, Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, Maryland, USA
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Cross-strand binding of TFAM to a single mtDNA molecule forms the mitochondrial nucleoid. Proc Natl Acad Sci U S A 2015; 112:11288-93. [PMID: 26305956 DOI: 10.1073/pnas.1512131112] [Citation(s) in RCA: 234] [Impact Index Per Article: 26.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Mammalian mitochondrial DNA (mtDNA) is packaged by mitochondrial transcription factor A (TFAM) into mitochondrial nucleoids that are of key importance in controlling the transmission and expression of mtDNA. Nucleoid ultrastructure is poorly defined, and therefore we used a combination of biochemistry, superresolution microscopy, and electron microscopy to show that mitochondrial nucleoids have an irregular ellipsoidal shape and typically contain a single copy of mtDNA. Rotary shadowing electron microscopy revealed that nucleoid formation in vitro is a multistep process initiated by TFAM aggregation and cross-strand binding. Superresolution microscopy of cultivated cells showed that increased mtDNA copy number increases nucleoid numbers without altering their sizes. Electron cryo-tomography visualized nucleoids at high resolution in isolated mammalian mitochondria and confirmed the sizes observed by superresolution microscopy of cell lines. We conclude that the fundamental organizational unit of the mitochondrial nucleoid is a single copy of mtDNA compacted by TFAM, and we suggest a packaging mechanism.
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Common mechanisms of DNA translocation motors in bacteria and viruses using one-way revolution mechanism without rotation. Biotechnol Adv 2015; 32:853-72. [PMID: 24913057 DOI: 10.1016/j.biotechadv.2014.01.006] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2013] [Revised: 01/24/2014] [Accepted: 01/25/2014] [Indexed: 12/15/2022]
Abstract
Biomotors were once described into two categories: linear motor and rotation motor. Recently, a third type of biomotor with revolution mechanism without rotation has been discovered. By analogy, rotation resembles the Earth rotating on its axis in a complete cycle every 24h, while revolution resembles the Earth revolving around the Sun one circle per 365 days (see animations http://nanobio.uky.edu/movie.html). The action of revolution that enables a motor free of coiling and torque has solved many puzzles and debates that have occurred throughout the history of viral DNA packaging motor studies. It also settles the discrepancies concerning the structure, stoichiometry, and functioning of DNA translocation motors. This review uses bacteriophages Phi29, HK97, SPP1, P22, T4, and T7 as well as bacterial DNA translocase FtsK and SpoIIIE or the large eukaryotic dsDNA viruses such as mimivirus and vaccinia virus as examples to elucidate the puzzles. These motors use ATPase, some of which have been confirmed to be a hexamer, to revolve around the dsDNA sequentially. ATP binding induces conformational change and possibly an entropy alteration in ATPase to a high affinity toward dsDNA; but ATP hydrolysis triggers another entropic and conformational change in ATPase to a low affinity for DNA, by which dsDNA is pushed toward an adjacent ATPase subunit. The rotation and revolution mechanisms can be distinguished by the size of channel: the channels of rotation motors are equal to or smaller than 2 nm, that is the size of dsDNA, whereas channels of revolution motors are larger than 3 nm. Rotation motors use parallel threads to operate with a right-handed channel, while revolution motors use a left-handed channel to drive the right-handed DNA in an anti-chiral arrangement. Coordination of several vector factors in the same direction makes viral DNA-packaging motors unusually powerful and effective. Revolution mechanism that avoids DNA coiling in translocating the lengthy genomic dsDNA helix could be advantageous for cell replication such as bacterial binary fission and cell mitosis without the need for topoisomerase or helicase to consume additional energy.
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Sokolova OS, Shaburova OV, Pechnikova EV, Shaytan AK, Krylov SV, Kiselev NA, Krylov VN. Genome packaging in EL and Lin68, two giant phiKZ-like bacteriophages of P. aeruginosa. Virology 2014; 468-470:472-478. [PMID: 25254945 DOI: 10.1016/j.virol.2014.09.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 06/01/2014] [Accepted: 09/04/2014] [Indexed: 10/24/2022]
Abstract
A unique feature of the Pseudomonas aeruginosa giant phage phiKZ is its way of genome packaging onto a spool-like protein structure, the inner body. Until recently, no similar structures have been detected in other phages. We have studied DNA packaging in P. aeruginosa phages EL and Lin68 using cryo-electron microscopy and revealed the presence of inner bodies. The shape and positioning of the inner body and the density of the DNA packaging in EL are different from those found in phiKZ and Lin68. This internal organization explains how the shorter EL genome is packed into a large EL capsid, which has the same external dimensions as the capsids of phiKZ and Lin68. The similarity in the structural organization in EL and other phiKZ-like phages indicates that EL is phylogenetically related to other phiKZ-like phages, and, despite the lack of detectable DNA homology, EL, phiKZ, and Lin68 descend from a common ancestor.
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Affiliation(s)
- O S Sokolova
- M.V. Lomonosov Moscow State University, Moscow, Russia; A.V. Shoubnikov Institute of Crystallography RAS, Moscow, Russia.
| | - O V Shaburova
- I.I. Mechnikov Research Institute of Vaccines and Sera, RAMS, Moscow, Russia
| | - E V Pechnikova
- A.V. Shoubnikov Institute of Crystallography RAS, Moscow, Russia
| | - A K Shaytan
- M.V. Lomonosov Moscow State University, Moscow, Russia
| | - S V Krylov
- I.I. Mechnikov Research Institute of Vaccines and Sera, RAMS, Moscow, Russia
| | - N A Kiselev
- A.V. Shoubnikov Institute of Crystallography RAS, Moscow, Russia
| | - V N Krylov
- I.I. Mechnikov Research Institute of Vaccines and Sera, RAMS, Moscow, Russia
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