101
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Abstract
Huge bacteriophages display genome sizes that bridge the gap between viral and bacterial genomes. Large Pseudomonas phages elaborate a nucleus-like structure in the infected bacterial cell and a tubulin-like phage protein forms a kind of spindle apparatus. While this probably represents cases of convergent evolution, these observations revive the discussion on the origin of eukaryotic cells.
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Affiliation(s)
- Harald Brüssow
- KU Leuven, Department of Biosystems, Laboratory of Gene Technology, Leuven, Belgium
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102
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA.
| | - Mart Krupovic
- Institut Pasteur, Archaeal Virology Unit, Department of Microbiology, Paris, France.
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103
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CRISPR Shields: Fending Off Diverse Cas Nucleases with Nucleus-like Structures. Mol Cell 2020; 77:934-936. [PMID: 32142691 DOI: 10.1016/j.molcel.2020.02.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Two recent studies have uncovered a novel means by which bacteriophages thwart host immunity. Mendoza et al. (2020) and Malone et al. (2020) demonstrate that a nucleus-like proteinaceous structure shields phage DNA from CRISPR-associated nucleases encompassing Cascade-Cas3, Cas9, and Cas12.
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104
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Luque D, Castón JR. Cryo-electron microscopy for the study of virus assembly. Nat Chem Biol 2020; 16:231-239. [PMID: 32080621 DOI: 10.1038/s41589-020-0477-1] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2019] [Accepted: 01/13/2020] [Indexed: 12/11/2022]
Abstract
Although viruses are extremely diverse in shape and size, evolution has led to a limited number of viral classes or lineages, which is probably linked to the assembly constraints of a viable capsid. Viral assembly mechanisms are restricted to two general pathways, (i) co-assembly of capsid proteins and single-stranded nucleic acids and (ii) a sequential mechanism in which scaffolding-mediated capsid precursor assembly is followed by genome packaging. Cryo-electron microscopy (cryo-EM) and cryo-electron tomography (cryo-ET), which are revolutionizing structural biology, are central to determining the high-resolution structures of many viral assemblies as well as those of assembly intermediates. This wealth of cryo-EM data has also led to the development and redesign of virus-based platforms for biomedical and biotechnological applications. In this Review, we will discuss recent viral assembly analyses by cryo-EM and cryo-ET showing how natural assembly mechanisms are used to encapsulate heterologous cargos including chemicals, enzymes, and/or nucleic acids for a variety of nanotechnological applications.
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Affiliation(s)
- Daniel Luque
- Centro Nacional de Microbiología/ISCIII, Majadahonda, Madrid, Spain
| | - José R Castón
- Department of Structure of Macromolecules, Centro Nacional de Biotecnología (CNB-CSIC), Campus Cantoblanco, Madrid, Spain.
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105
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Thammatinna K, Egan ME, Htoo HH, Khanna K, Sugie J, Nideffer JF, Villa E, Tassanakajon A, Pogliano J, Nonejuie P, Chaikeeratisak V. A novel vibriophage exhibits inhibitory activity against host protein synthesis machinery. Sci Rep 2020; 10:2347. [PMID: 32047244 PMCID: PMC7012835 DOI: 10.1038/s41598-020-59396-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2019] [Accepted: 01/27/2020] [Indexed: 12/27/2022] Open
Abstract
Since the emergence of deadly pathogens and multidrug-resistant bacteria at an alarmingly increased rate, bacteriophages have been developed as a controlling bioagent to prevent the spread of pathogenic bacteria. One of these pathogens, disease-causing Vibrio parahaemolyticus (VPAHPND) which induces acute hepatopancreatic necrosis, is considered one of the deadliest shrimp pathogens, and has recently become resistant to various classes of antibiotics. Here, we discovered a novel vibriophage that specifically targets the vibrio host, VPAHPND. The vibriophage, designated Seahorse, was classified in the family Siphoviridae because of its icosahedral capsid surrounded by head fibers and a non-contractile long tail. Phage Seahorse was able to infect the host in a broad range of pH and temperatures, and it had a relatively short latent period (nearly 30 minutes) in which it produced progeny at 72 particles per cell at the end of its lytic cycle. Upon phage infection, the host nucleoid condensed and became toroidal, similar to the bacterial DNA morphology seen during tetracycline treatment, suggesting that phage Seahorse hijacked host biosynthesis pathways through protein translation. As phage Seahorse genome encodes 48 open reading frames with many hypothetical proteins, this genome could be a potential untapped resource for the discovery of phage-derived therapeutic proteins.
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Affiliation(s)
- Khrongkhwan Thammatinna
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - MacKennon E Egan
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Htut Htut Htoo
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Kanika Khanna
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Joseph Sugie
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Jason F Nideffer
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Elizabeth Villa
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Anchalee Tassanakajon
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Poochit Nonejuie
- Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand
| | - Vorrapon Chaikeeratisak
- Center of Excellence for Molecular Biology and Genomics of Shrimp, Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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106
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Al-Shayeb B, Sachdeva R, Chen LX, Ward F, Munk P, Devoto A, Castelle CJ, Olm MR, Bouma-Gregson K, Amano Y, He C, Méheust R, Brooks B, Thomas A, Lavy A, Matheus-Carnevali P, Sun C, Goltsman DSA, Borton MA, Sharrar A, Jaffe AL, Nelson TC, Kantor R, Keren R, Lane KR, Farag IF, Lei S, Finstad K, Amundson R, Anantharaman K, Zhou J, Probst AJ, Power ME, Tringe SG, Li WJ, Wrighton K, Harrison S, Morowitz M, Relman DA, Doudna JA, Lehours AC, Warren L, Cate JHD, Santini JM, Banfield JF. Clades of huge phages from across Earth's ecosystems. Nature 2020; 578:425-431. [PMID: 32051592 PMCID: PMC7162821 DOI: 10.1038/s41586-020-2007-4] [Citation(s) in RCA: 234] [Impact Index Per Article: 58.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Accepted: 01/02/2020] [Indexed: 12/31/2022]
Abstract
Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.
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Affiliation(s)
- Basem Al-Shayeb
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Rohan Sachdeva
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Lin-Xing Chen
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Fred Ward
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Patrick Munk
- National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Audra Devoto
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Cindy J Castelle
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Matthew R Olm
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Keith Bouma-Gregson
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Yuki Amano
- Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai-mura, Japan
| | - Christine He
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Raphaël Méheust
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Brandon Brooks
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Alex Thomas
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Adi Lavy
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | | | - Christine Sun
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | | | - Mikayla A Borton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Allison Sharrar
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Alexander L Jaffe
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Tara C Nelson
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Rose Kantor
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ray Keren
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Katherine R Lane
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Ibrahim F Farag
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Shufei Lei
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | - Kari Finstad
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Ronald Amundson
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA
| | - Karthik Anantharaman
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA
| | | | - Alexander J Probst
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Mary E Power
- Integrative Biology, University of California Berkeley, Berkeley, CA, USA
| | | | - Wen-Jun Li
- School of Life Sciences, Sun Yat-Sen University, Guangzhou, China
| | - Kelly Wrighton
- Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA
| | - Sue Harrison
- Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa
| | - Michael Morowitz
- Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - David A Relman
- Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA
| | - Jennifer A Doudna
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Anne-Catherine Lehours
- Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, CNRS, Clermont-Ferrand, France
| | - Lesley Warren
- Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada
| | - Jamie H D Cate
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA
| | - Joanne M Santini
- Institute of Structural and Molecular Biology, University College London, London, UK
| | - Jillian F Banfield
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
- Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA.
- Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
- School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia.
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107
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The arms race between bacteria and their phage foes. Nature 2020; 577:327-336. [PMID: 31942051 DOI: 10.1038/s41586-019-1894-8] [Citation(s) in RCA: 403] [Impact Index Per Article: 100.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Accepted: 11/13/2019] [Indexed: 12/26/2022]
Abstract
Bacteria are under immense evolutionary pressure from their viral invaders-bacteriophages. Bacteria have evolved numerous immune mechanisms, both innate and adaptive, to cope with this pressure. The discovery and exploitation of CRISPR-Cas systems have stimulated a resurgence in the identification and characterization of anti-phage mechanisms. Bacteriophages use an extensive battery of counter-defence strategies to co-exist in the presence of these diverse phage defence mechanisms. Understanding the dynamics of the interactions between these microorganisms has implications for phage-based therapies, microbial ecology and evolution, and the development of new biotechnological tools. Here we review the spectrum of anti-phage systems and highlight their evasion by bacteriophages.
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108
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Ryan F. Viral Symbiosis in the Origins and Evolution of Life with a Particular Focus on the Placental Mammals. Results Probl Cell Differ 2020; 69:3-24. [PMID: 33263867 DOI: 10.1007/978-3-030-51849-3_1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Advances in understanding over the last decade or so highlight the need for a reappraisal of the role of viruses in relation to the origins and evolution of cellular life, as well as in the homeostasis of the biosphere on which all of life depends. The relevant advances have, in particular, revealed an important contribution of viruses to the evolution of the placental mammals, while also contributing key roles to mammalian embryogenesis, genomic evolution, and physiology. Part of this reappraisal will include the origins of viruses, a redefinition of their quintessential nature, and a suggestion as to how we might view viruses in relation to the tree of life.
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Affiliation(s)
- Frank Ryan
- The Academic Unit of Medical Education, Faculty of Medicine, Dentistry and Health, The University of Sheffield, Sheffield, UK.
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109
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Al-Naamani N, Ali I. Packing of semiflexible polymers into viral capsid in crowded environments. Phys Rev E 2019; 100:052412. [PMID: 31869914 DOI: 10.1103/physreve.100.052412] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Indexed: 11/07/2022]
Abstract
We use coarse-grained Langevin dynamics simulations to study packing of semiflexible polymers into a spherical capsid, with and without a tail, inside a crowded cell. We use neutral and charged, but highly screened, polymers and compare packing rates of the two. Such packing conditions are relevant, for example, to λ DNA packing inside Escherichia coli bacterial cells, where the crowd particles are proteins, bacterial DNA, and salts. For a neutral polymer packing into a capsid with a tail, attractive interactions with the crowd particles make packing slightly harder at higher crowd densities, but repulsive interactions make it easier. Our results indicate that packing into a tailless capsid is less efficient at low crowd densities than into one with a long tail. However, this trend becomes opposite at higher densities. In addition, packing into a capsid with a long tail shows a highly variable waiting time before packing initiates, a feature absent for a tailless capsid. Electrical interactions at physiological conditions do not have much effect. Some bacterial cells, such as Pseudomonas chlororaphis, form a nucleuslike structure encapsulating the phage 201ϕ2-1 DNA. We also study here the packing dynamics with the nucleus present. We find packing is faster compared to the case of no-nucleus packing. We also observe knot formations but these knots untangle quickly while the polymer translocates. This knot formation is independent of polymer charge and presence of crowd particles.
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Affiliation(s)
- N Al-Naamani
- Department of Physics, College of Science, P.O. Box 36, Sultan Qaboos University, Al-Khod 123, Oman
| | - I Ali
- Department of Physics, College of Science, P.O. Box 36, Sultan Qaboos University, Al-Khod 123, Oman
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110
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A jumbo phage that forms a nucleus-like structure evades CRISPR-Cas DNA targeting but is vulnerable to type III RNA-based immunity. Nat Microbiol 2019; 5:48-55. [PMID: 31819217 DOI: 10.1038/s41564-019-0612-5] [Citation(s) in RCA: 103] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 10/17/2019] [Indexed: 12/26/2022]
Abstract
CRISPR-Cas systems provide bacteria with adaptive immunity against bacteriophages1. However, DNA modification2,3, the production of anti-CRISPR proteins4,5 and potentially other strategies enable phages to evade CRISPR-Cas. Here, we discovered a Serratia jumbo phage that evades type I CRISPR-Cas systems, but is sensitive to type III immunity. Jumbo phage infection resulted in a nucleus-like structure enclosed by a proteinaceous phage shell-a phenomenon only reported recently for distantly related Pseudomonas phages6,7. All three native CRISPR-Cas complexes in Serratia-type I-E, I-F and III-A-were spatially excluded from the phage nucleus and phage DNA was not targeted. However, the type III-A system still arrested jumbo phage infection by targeting phage RNA in the cytoplasm in a process requiring Cas7, Cas10 and an accessory nuclease. Type III, but not type I, systems frequently targeted nucleus-forming jumbo phages that were identified in global viral sequence datasets. The ability to recognize jumbo phage RNA and elicit immunity probably contributes to the presence of both RNA- and DNA-targeting CRISPR-Cas systems in many bacteria1,8. Together, our results support the model that jumbo phage nucleus-like compartments serve as a barrier to DNA-targeting, but not RNA-targeting, defences, and that this phenomenon is widespread among jumbo phages.
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111
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Mendoza SD, Nieweglowska ES, Govindarajan S, Leon LM, Berry JD, Tiwari A, Chaikeeratisak V, Pogliano J, Agard DA, Bondy-Denomy J. A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases. Nature 2019; 577:244-248. [PMID: 31819262 PMCID: PMC6949375 DOI: 10.1038/s41586-019-1786-y] [Citation(s) in RCA: 119] [Impact Index Per Article: 23.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/11/2019] [Indexed: 11/09/2022]
Abstract
All viruses require strategies to inhibit or evade the immunity pathways of cells they infect. The viruses that infect bacteria, bacteriophages (phages), must avoid nucleic-acid targeting immune pathways such as CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes) and restriction-modification (R-M) systems to replicate efficiently1. Here, we show that jumbo phage ΦKZ, infecting Pseudomonas aeruginosa, segregates its DNA from immunity nucleases by constructing a proteinaceous nucleus-like compartment. ΦKZ resists many DNA-targeting immune systems in vivo, including two CRISPR-Cas3 subtypes, Cas9, Cas12a, and the restriction enzymes HsdRMS and EcoRI. Cas and restriction enzymes are unable to access the phage DNA throughout the infection, but engineered re-localization of EcoRI inside the compartment enables phage targeting and cell protection. Moreover, ΦKZ is sensitive to the RNA targeting CRISPR-Cas enzyme, Cas13a, likely due to phage mRNA localizing to the cytoplasm. Collectively, we propose that Pseudomonas jumbo phages evade a broad spectrum of DNA-targeting nucleases through the assembly of a protein barrier around their genome.
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Affiliation(s)
- Senén D Mendoza
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Eliza S Nieweglowska
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA
| | - Sutharsan Govindarajan
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA.,Department of Biology, SRM University AP, Amaravati, India
| | - Lina M Leon
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Joel D Berry
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Anika Tiwari
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA
| | - Vorrapon Chaikeeratisak
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA.,Department of Biochemistry, Faculty of Science, Chulalongkorn University, Bangkok, Thailand
| | - Joe Pogliano
- Division of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - David A Agard
- Howard Hughes Medical Institute, Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA, USA.,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology, University of California San Francisco, San Francisco, CA, USA. .,Quantitative Biosciences Institute, University of California San Francisco, San Francisco, CA, USA.
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112
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Imam M, Alrashid B, Patel F, Dowah ASA, Brown N, Millard A, Clokie MRJ, Galyov EE. vB_PaeM_MIJ3, a Novel Jumbo Phage Infecting Pseudomonas aeruginosa, Possesses Unusual Genomic Features. Front Microbiol 2019; 10:2772. [PMID: 31849908 PMCID: PMC6892783 DOI: 10.3389/fmicb.2019.02772] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 11/13/2019] [Indexed: 01/06/2023] Open
Abstract
Phages are the most abundant biological entity on Earth. There are many variants in phage virion sizes, morphology, and genome sizes. Large virion sized phages, with genome sizes greater than 200 kbp have been identified and termed as Jumbo phages. These phages exhibit certain characteristics that have not been reported in phages with smaller genomes. In this work, a jumbo phage named MIJ3 (vB_PaeM_MIJ3) that infects Pseudomonas aeruginosa PAO1 was isolated from an equine livery yard in Leicestershire, United Kingdom. The genome and biological characteristics of this phage have been investigated. MIJ3 is a Myovirus with multiple long tail fibers. Assessment of the host range of MIJ3 revealed that it has the ability to infect many clinical isolates of P. aeruginosa. Bioinformatics analysis of the phage genome indicated that MIJ3 is closely related to the Pseudomonas phage, PA5oct. MIJ3 possesses several unusual features that are either rarely present in other phages or have not yet been reported. In particular, MIJ3 encodes a FtsH-like protein, and a putative lysidine synthase, TilS. These two proteins have not been reported in phages. MIJ3 also possesses a split DNA polymerase B with a novel intein. Of particular interest, unlike other jumbo phages infecting Pseudomonas spp., MIJ3 lacks the genetic elements required for the formation of the phage nucleus, which was believed to be conserved across jumbo Pseudomonas phages.
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Affiliation(s)
- Mohammed Imam
- Department of Respiratory Sciences, College of Life Sciences, University of Leicester, Leicester, United Kingdom.,Laboratory Department, University Medical Center, Umm Al-Qura University, Mecca, Saudi Arabia
| | - Bandar Alrashid
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom.,King Faisal Specialist Hospital and Research Centre, Riyadh, Saudi Arabia
| | - Faizal Patel
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Ahmed S A Dowah
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Nathan Brown
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Andrew Millard
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Martha R J Clokie
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
| | - Edouard E Galyov
- Department of Genetics and Genome Biology, College of Life Sciences, University of Leicester, Leicester, United Kingdom
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113
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Olszak T, Danis-Wlodarczyk K, Arabski M, Gula G, Maciejewska B, Wasik S, Lood C, Higgins G, Harvey BJ, Lavigne R, Drulis-Kawa Z. Pseudomonas aeruginosa PA5oct Jumbo Phage Impacts Planktonic and Biofilm Population and Reduces Its Host Virulence. Viruses 2019; 11:E1089. [PMID: 31771160 PMCID: PMC6950013 DOI: 10.3390/v11121089] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 11/19/2019] [Accepted: 11/20/2019] [Indexed: 12/20/2022] Open
Abstract
The emergence of phage-resistant mutants is a key aspect of lytic phages-bacteria interaction and the main driver for the co-evolution between both organisms. Here, we analyze the impact of PA5oct jumbo phage treatment on planktonic/cell line associated and sessile P. aeruginosa population. Besides its broad-spectrum activity and efficient bacteria reduction in both airway surface liquid (ASL) model, and biofilm matrix degradation, PA5oct appears to persist in most of phage-resistant clones. Indeed, a high percentage of resistance (20/30 clones) to PA5oct is accompanied by the presence of phage DNA within bacterial culture. Moreover, the maintenance of this phage in the bacterial population correlates with reduced P. aeruginosa virulence, coupled with a sensitization to innate immune mechanisms, and a significantly reduced growth rate. We observed rather unusual consequences of PA5oct infection causing an increased inflammatory response of monocytes to P. aeruginosa. This phenomenon, combined with the loss or modification of the phage receptor, makes most of the phage-resistant clones significantly less pathogenic in in vivo model. These findings provide new insights into the general knowledge of giant phages biology and the impact of their application in phage therapy.
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Affiliation(s)
- Tomasz Olszak
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Katarzyna Danis-Wlodarczyk
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Michal Arabski
- Department of Biochemistry and Genetics, Institute of Biology, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Grzegorz Gula
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Barbara Maciejewska
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
| | - Slawomir Wasik
- Department of Molecular Physics, Institute of Physics, The Jan Kochanowski University in Kielce, 25-406 Kielce, Poland;
| | - Cédric Lood
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
- Laboratory of Computational Systems Biology, KU Leuven, 3000 Leuven, Belgium
| | - Gerard Higgins
- National Children Research Centre, Our Lady’s Children’s Hospital, Crumlin, 12 Dublin, Ireland;
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Brian J. Harvey
- Department of Molecular Medicine, Royal College of Surgeons in Ireland, Education and Research Centre, Beaumont Hospital, 9 Dublin, Ireland;
| | - Rob Lavigne
- Laboratory of Gene Technology, KU Leuven, 3001 Heverlee, Belgium; (C.L.); (R.L.)
| | - Zuzanna Drulis-Kawa
- Department of Pathogen Biology and Immunology, Institute of Genetics and Microbiology, University of Wroclaw, 51-148 Wroclaw, Poland; (T.O.); (K.D.-W.); (G.G.); (B.M.)
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114
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Poole AM, Hendrickson HL. Response: Commentary: Manifold Routes to a Nucleus. Front Microbiol 2019; 10:2585. [PMID: 31781075 PMCID: PMC6857541 DOI: 10.3389/fmicb.2019.02585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/24/2019] [Indexed: 11/18/2022] Open
Affiliation(s)
- Anthony M Poole
- School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Heather L Hendrickson
- School of Natural and Computational Sciences, Massey University, Auckland, New Zealand
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115
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Mind the gap: Micro-expansion joints drastically decrease the bending of FIB-milled cryo-lamellae. J Struct Biol 2019; 208:107389. [PMID: 31536774 DOI: 10.1016/j.jsb.2019.09.006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Revised: 08/21/2019] [Accepted: 09/14/2019] [Indexed: 11/22/2022]
Abstract
Cryo-focused ion beam (FIB)-milling of biological samples can be used to generate thin electron-transparent slices from cells grown or deposited on EM grids. These so called cryo-lamellae allow high-resolution structural studies of the natural cellular environment by in situ cryo-electron tomography. However, the cryo-lamella workflow is a low-throughput technique and can easily be hindered by technical issues like the bending of the lamellae during the final cryo-FIB-milling steps. The severity of lamella bending seems to correlate with crinkling of the EM grid support film at cryogenic temperatures, which could generate tensions that may be transferred onto the thin lamella, leading to its bending and breakage. To protect the lamellae from such forces, we milled "micro-expansion joints" alongside the lamellae, creating gaps in the support that can act as physical buffers to safely absorb material motion. We demonstrate that the presence of micro-expansion joints drastically decreases bending of lamellae milled from eukaryotic cells grown and frozen on EM grids. Furthermore, we show that this adaptation does not create additional instabilities that could impede subsequent parts of the cryo-lamella workflow, as we obtained high-quality Volta phase plate tomograms revealing macromolecules in their natural structural context. The minimal additional effort required to implement micro-expansion joints in the cryo-FIB-milling workflow makes them a straightforward solution against cryo-lamella bending to increase the throughput of in situ structural biology studies.
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116
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Coulibaly F. Polyhedra, spindles, phage nucleus and pyramids: Structural biology of viral superstructures. Adv Virus Res 2019; 105:275-335. [PMID: 31522707 DOI: 10.1016/bs.aivir.2019.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Viral infection causes comprehensive rearrangements of the cell that reflect as much host defense mechanisms as virus-induced structures assembled to facilitate infection. Regardless of their pro- or antiviral role, large intracellular structures are readily detectable by microscopy and often provide a signature characteristic of a specific viral infection. The structural features and localization of these assemblies have thus been commonly used for the diagnostic and classification of viruses since the early days of virology. More recently, characterization of viral superstructures using molecular and structural approaches have revealed very diverse organizations and roles, ranging from dynamic viral factories behaving like liquid organelles to ultra-stable crystals embedding and protecting virions. This chapter reviews the structures, functions and biotechnological applications of virus-induced superstructures with a focus on assemblies that have a regular organization, for which detailed structural descriptions are available. Examples span viruses infecting all domains of life including the assembly of virions into crystalline arrays in eukaryotic and bacterial viruses, nucleus-like compartments involved in the replication of large bacteriophages, and pyramid-like structures mediating the egress of archaeal viruses. Among these superstructures, high-resolution structures are available for crystalline objects produced by insect viruses: viral polyhedra which function as the infectious form of occluded viruses, and spindles which are potent virulence factors of entomopoxviruses. In turn, some of these highly symmetrical objects have been used to develop and validate advanced structural approaches, pushing the boundary of structural biology.
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Affiliation(s)
- Fasséli Coulibaly
- Infection & Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Clayton, VIC, Australia.
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117
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Khanna K, Lopez-Garrido J, Zhao Z, Watanabe R, Yuan Y, Sugie J, Pogliano K, Villa E. The molecular architecture of engulfment during Bacillus subtilis sporulation. eLife 2019; 8:45257. [PMID: 31282858 PMCID: PMC6684271 DOI: 10.7554/elife.45257] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 07/04/2019] [Indexed: 01/08/2023] Open
Abstract
The study of bacterial cell biology is limited by difficulties in visualizing cellular structures at high spatial resolution within their native milieu. Here, we visualize Bacillus subtilis sporulation using cryo-electron tomography coupled with cryo-focused ion beam milling, allowing the reconstruction of native-state cellular sections at molecular resolution. During sporulation, an asymmetrically-positioned septum generates a larger mother cell and a smaller forespore. Subsequently, the mother cell engulfs the forespore. We show that the septal peptidoglycan is not completely degraded at the onset of engulfment. Instead, the septum is uniformly and only slightly thinned as it curves towards the mother cell. Then, the mother cell membrane migrates around the forespore in tiny finger-like projections, whose formation requires the mother cell SpoIIDMP protein complex. We propose that a limited number of SpoIIDMP complexes tether to and degrade the peptidoglycan ahead of the engulfing membrane, generating an irregular membrane front.
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Affiliation(s)
- Kanika Khanna
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Javier Lopez-Garrido
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Ziyi Zhao
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Reika Watanabe
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Yuan Yuan
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Joseph Sugie
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Kit Pogliano
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
| | - Elizabeth Villa
- Division of Biological SciencesUniversity of California, San DiegoLa JollaUnited States
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118
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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.
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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.
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119
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Wojtus JK, Frampton RA, Warring S, Hendrickson H, Fineran PC. Genome Sequence of a Jumbo Bacteriophage That Infects the Kiwifruit Phytopathogen Pseudomonas syringae pv. actinidiae. Microbiol Resour Announc 2019; 8:e00224-19. [PMID: 31147429 PMCID: PMC6544186 DOI: 10.1128/mra.00224-19] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 05/06/2019] [Indexed: 12/24/2022] Open
Abstract
Bacteriophage ϕPsa21 is a potential biocontrol agent that infects the kiwifruit phytopathogen Pseudomonas syringae pv. actinidiae. ϕPsa21 is a "jumbo" phage with a genome of ∼305 kb. Here, we present the genome sequence of ϕPsa21 and discuss potential genes indicative of the formation of nucleoid structures during viral replication.
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Affiliation(s)
- Joanna K Wojtus
- Massey Phage Whānau, School of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
- School of Life Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Rebekah A Frampton
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- The New Zealand Institute for Plant and Food Research Limited, Lincoln, New Zealand
| | - Suzanne Warring
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
| | - Heather Hendrickson
- Massey Phage Whānau, School of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Peter C Fineran
- Department of Microbiology and Immunology, University of Otago, Dunedin, New Zealand
- Bio-Protection Research Centre, University of Otago, Dunedin, New Zealand
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120
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Virus capsid assembly across different length scales inspire the development of virus-based biomaterials. Curr Opin Virol 2019; 36:38-46. [PMID: 31071601 DOI: 10.1016/j.coviro.2019.02.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2018] [Revised: 02/12/2019] [Accepted: 02/25/2019] [Indexed: 01/26/2023]
Abstract
In biology, there are an abundant number of self-assembled structures organized according to hierarchical levels of complexity. In some examples, the assemblies formed at each level exhibit unique properties and behaviors not present in individual components. Viruses are an example of such where first individual subunits come together to form a capsid structure, some utilizing a scaffolding protein to template or catalyze the capsid formation. Increasing the level of complexity, the viral capsids can then be used as building blocks of higher-level assemblies. This has inspired scientists to design and construct virus capsid-based functional nano-materials. This review provides some insight into the assembly of virus capsids across several length scales, and certain properties that arise at different levels, providing examples found in naturally occurring systems and those that are synthetically designed.
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121
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Abstract
Bacteriophages, discovered about a century ago, have been pivotal as models for understanding the fundamental principles of molecular biology. While interest in phage biology declined after the phage "golden era," key recent developments, including advances in phage genomics, microscopy, and the discovery of the CRISPR-Cas anti-phage defense system, have sparked a renaissance in phage research in the past decade. This review highlights recently discovered unexpected complexities in phage biology, describes a new arsenal of phage genes that help them overcome bacterial defenses, and discusses advances toward documentation of the phage biodiversity on a global scale.
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Affiliation(s)
- Gal Ofir
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Rotem Sorek
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel.
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122
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123
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Bárdy P, Hrebík D, Pantůček R, Plevka P. Future prospects of structural studies to advance our understanding of phage biology. MICROBIOLOGY AUSTRALIA 2019. [DOI: 10.1071/ma19009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Bacteriophages, being the most abundant biological entities on the Earth, play a major role in regulating populations of bacteria and thus influence the evolution and stability of ecosystems. Phage infections of pathogenic bacteria can both exacerbate and alleviate the severity of the disease. The structural characterisations of phage particles and individual proteins have enabled the understanding of many aspects of phage biology. Due to methodological limitations, most of the structures were determined from purified samples in vitro. However, studies performed outside the cellular context cannot capture the complex and dynamic interactions of the macromolecules that are required for their biological functions. Current developments in structural biology, in particular cryo-electron microscopy, allow in situ high-resolution studies of phage-infected cells. Here we discuss open questions in phage biology that could be addressed by structural biology techniques and their potential to enable the use of tailed phages in industrial applications and human therapy.
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124
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Nikolic J, Lagaudrière-Gesbert C, Scrima N, Blondel D, Gaudin Y. Structure and Function of Negri Bodies. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:111-127. [PMID: 31317498 DOI: 10.1007/978-3-030-14741-9_6] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Replication and assembly of many viruses occur in viral factories which are specialized intracellular compartments formed during viral infection. For rabies virus, those viral factories are called Negri bodies (NBs). NBs are cytoplasmic inclusion bodies in which viral RNAs (mRNAs as well as genomic and antigenomic RNAs) are synthesized. NBs are spherical, they can fuse together, and can reversibly deform when encountering a physical barrier. All these characteristics are similar to those of eukaryotic membrane-less liquid organelles which contribute to the compartmentalization of the cell interior. Indeed, the liquid nature of NBs has been confirmed by FRAP experiments. The co-expression of rabies virus nucleoprotein N and phosphoprotein P is sufficient to induce the formation of cytoplasmic inclusions recapitulating NBs properties. Remarkably, P and N have features similar to those of cellular proteins involved in liquid organelles formation: N is an RNA-binding protein and P contains intrinsically disordered domains. An overview of the literature indicates that formation of liquid viral factories by phase separation is probably common among Mononegavirales. This allows specific recruitment and concentration of viral proteins. Finally, as virus-associated molecular patterns recognized by cellular sensors of RNA virus replication are probably essentially present in the viral factory, there should be a subtle interplay (which remains to be characterized) between those liquid structures and the cellular proteins which trigger the innate immune response.
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Affiliation(s)
- Jovan Nikolic
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Cécile Lagaudrière-Gesbert
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Nathalie Scrima
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France
| | - Danielle Blondel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France.
| | - Yves Gaudin
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Gif-sur-Yvette cedex, France.
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125
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Abstract
It is widely assumed that there is a clear distinction between eukaryotes, with cell nuclei, and prokaryotes, which lack nuclei. This suggests the evolution of nuclear compartmentation is a singular event. However, emerging knowledge of the diversity of bacterial internal cell structures suggests the picture may not be as black-and-white as previously thought. For instance, some members of the bacterial PVC superphylum appear to have nucleus-like compartmentation, where transcription and translation are physically separated, and some jumbophages have recently been shown to create nucleus-like structures within their Pseudomonad hosts. Moreover, there is also tantalizing metagenomic identification of new Archaea that carry homologs of genes associated with internal cell membrane structure in eukaryotes. All these cases invite comparison with eukaryote cell biology. While the bacterial cases of genetic compartmentation are likely convergent, and thus viewed by many as not germane to the question of eukaryote origins, we argue here that, in addressing the broader question of the evolution of compartmentation, other instances are at least as important: they provide us with a point of comparison which is critical for a more general understanding of both the conditions favoring the emergence of intracellular compartmentation of DNA and the evolutionary consequences of such cellular architecture. Finally, we consider three classes of explanation for the emergence of compartmentation: physical protection, crosstalk avoidance and nonadaptive origins.
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Affiliation(s)
- Heather L. Hendrickson
- Institute of Natural and Mathematical Sciences, Massey University, Auckland, New Zealand
| | - Anthony M. Poole
- Bioinformatics Institute, The University of Auckland, Auckland, New Zealand
- Te Ao Mârama/Centre for Fundamental Inquiry, The University of Auckland, Auckland, New Zealand
- School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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126
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Pfeffer S, Mahamid J. Unravelling molecular complexity in structural cell biology. Curr Opin Struct Biol 2018; 52:111-118. [PMID: 30339965 DOI: 10.1016/j.sbi.2018.08.009] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 06/18/2018] [Accepted: 08/29/2018] [Indexed: 12/14/2022]
Abstract
Structural and cell biology have traditionally been separate disciplines and employed techniques that were well defined within the realm of either one or the other. Recent technological breakthroughs propelled electron microscopy of frozen hydrated specimens (cryo-EM) followed by single-particle analysis (SPA) to become a widely applied approach for obtaining near-atomic resolution structures of purified macromolecules. In parallel, ongoing developments on sample preparation are increasingly successful in bringing molecular views into cell biology. Cryo-electron tomography (cryo-ET) has so far served as the main imaging modality employed in these efforts towards obtaining three-dimensional (3D) volumes of heterogeneous molecular assemblies. We review the state-of-the-art in cryo-ET and computational processing and describe the current opportunities and frontiers for in-cell applications.
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Affiliation(s)
- Stefan Pfeffer
- Centre for Molecular Biology of Heidelberg University (ZMBH), 69120 Heidelberg, Germany
| | - Julia Mahamid
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, 69117 Heidelberg, Germany.
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127
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Sun Y, Yao Y, Wang H, Fu W, Chen C, Saha ML, Zhang M, Datta S, Zhou Z, Yu H, Li X, Stang PJ. Self-Assembly of Metallacages into Multidimensional Suprastructures with Tunable Emissions. J Am Chem Soc 2018; 140:12819-12828. [PMID: 30212221 PMCID: PMC6372098 DOI: 10.1021/jacs.8b05809] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Cubic metallacages were arranged into multidimensional (one-, two-, and three-dimensional) suprastructures via multistep assembly. Four new shape-controllable, hybrid metallacages with modified substituents and tunable electronic properties were prepared using dicarboxylate ligands with various substituents (sodium sulfonate, nitro, methoxyl, and amine), tetra-(4-pyridylphenyl) ethylene, and cis-(PEt3)2Pt(OTf)2. The as-prepared metallacages were used as building blocks for further assembly. Diverse suprastructures with tunable emissions (λmax from 451 to 519 nm) and various substituents (-SO3Na, -NO2, -OCH3, and -NH2) were prepared depending on the substituents and solvents used.
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Affiliation(s)
- Yan Sun
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
- School of Chemistry and Chemical Engineering, Yangzhou University, Yangzhou, Jiangsu 225002, PR China
| | - Yong Yao
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Heng Wang
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Wenxin Fu
- Beijing National Laboratory for Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences, Beijing 100190, PR China
| | - Chongyi Chen
- Ningbo Key Laboratory of Specialty Polymers, Faculty of Materials Science and Chemical Engineering, Ningbo University, Ningbo, Zhejiang 315211, PR China
| | - Manik Lal Saha
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Mingming Zhang
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Sougata Datta
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Zhixuan Zhou
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Huaxu Yu
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
| | - Xiaopeng Li
- Department of Chemistry, University of South Florida, 4202 East Fowler Avenue, Tampa, Florida 33620, United States
| | - Peter. J. Stang
- Department of Chemistry, University of Utah, 315 South 1400 East, Room 2020, Salt Lake City, Utah 84112, United States
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128
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Scutigliani EM, Scholl ER, Grootemaat AE, Khanal S, Kochan JA, Krawczyk PM, Reits EA, Garzan A, Ngo HX, Green KD, Garneau-Tsodikova S, Ruijter JM, van Veen HA, van der Wel NN. Interfering With DNA Decondensation as a Strategy Against Mycobacteria. Front Microbiol 2018; 9:2034. [PMID: 30233521 PMCID: PMC6135046 DOI: 10.3389/fmicb.2018.02034] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2018] [Accepted: 08/13/2018] [Indexed: 12/31/2022] Open
Abstract
Tuberculosis is once again a major global threat, leading to more than 1 million deaths each year. Treatment options for tuberculosis patients are limited, expensive and characterized by severe side effects, especially in the case of multidrug-resistant forms. Uncovering novel vulnerabilities of the pathogen is crucial to generate new therapeutic strategies. Using high resolution microscopy techniques, we discovered one such vulnerability of Mycobacterium tuberculosis. We demonstrate that the DNA of M. tuberculosis can condense under stressful conditions such as starvation and antibiotic treatment. The DNA condensation is reversible and specific for viable bacteria. Based on these observations, we hypothesized that blocking the recovery from the condensed state could weaken the bacteria. We showed that after inducing DNA condensation, and subsequent blocking of acetylation of DNA binding proteins, the DNA localization in the bacteria is altered. Importantly under these conditions, Mycobacterium smegmatis did not replicate and its survival was significantly reduced. Our work demonstrates that agents that block recovery from the condensed state of the nucleoid can be exploited as antibiotic. The combination of fusidic acid and inhibition of acetylation of DNA binding proteins, via the Eis enzyme, potentiate the efficacy of fusidic acid by 10 and the Eis inhibitor to 1,000-fold. Hence, we propose that successive treatment with antibiotics and drugs interfering with recovery from DNA condensation constitutes a novel approach for treatment of tuberculosis and related bacterial infections.
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Affiliation(s)
- Enzo M Scutigliani
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Edwin R Scholl
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Anita E Grootemaat
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Sadhana Khanal
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Jakub A Kochan
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | | | - Eric A Reits
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Atefeh Garzan
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | - Huy X Ngo
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | - Keith D Green
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY, United States
| | | | - Jan M Ruijter
- Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Henk A van Veen
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
| | - Nicole N van der Wel
- Electron Microscopy Center Amsterdam, Academic Medical Center, Amsterdam UMC, University of Amsterdam, Amsterdam, Netherlands.,Medical Biology, Academic Medical Center, Amsterdam, Netherlands
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129
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de Jonge PA, Nobrega FL, Brouns SJJ, Dutilh BE. Molecular and Evolutionary Determinants of Bacteriophage Host Range. Trends Microbiol 2018; 27:51-63. [PMID: 30181062 DOI: 10.1016/j.tim.2018.08.006] [Citation(s) in RCA: 214] [Impact Index Per Article: 35.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 07/07/2018] [Accepted: 08/13/2018] [Indexed: 01/12/2023]
Abstract
The host range of a bacteriophage is the taxonomic diversity of hosts it can successfully infect. Host range, one of the central traits to understand in phages, is determined by a range of molecular interactions between phage and host throughout the infection cycle. While many well studied model phages seem to exhibit a narrow host range, recent ecological and metagenomics studies indicate that phages may have specificities that range from narrow to broad. There is a growing body of studies on the molecular mechanisms that enable phages to infect multiple hosts. These mechanisms, and their evolution, are of considerable importance to understanding phage ecology and the various clinical, industrial, and biotechnological applications of phage. Here we review knowledge of the molecular mechanisms that determine host range, provide a framework defining broad host range in an evolutionary context, and highlight areas for additional research.
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Affiliation(s)
- Patrick A de Jonge
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands
| | - Franklin L Nobrega
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands
| | - Stan J J Brouns
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Van der Maasweg 9 2629 HZ, Delft, The Netherlands; Laboratory for Microbiology, Wageningen University, Stippeneng 4 6708 WE, Wageningen, The Netherlands; These authors made equal contributions
| | - Bas E Dutilh
- Theoretical Biology and Bioinformatics, Utrecht University, Padualaan 8 3584 CH Utrecht, The Netherlands; Centre for Molecular and Biomolecular Informatics, Radboud University Medical Centre, Geert Grooteplein Zuid 26-28, 6525GA Nijmegen, The Netherlands; These authors made equal contributions.
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130
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Melia CE, Bharat TAM. Locating macromolecules and determining structures inside bacterial cells using electron cryotomography. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2018; 1866:973-981. [PMID: 29908328 PMCID: PMC6052677 DOI: 10.1016/j.bbapap.2018.06.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Revised: 05/30/2018] [Accepted: 06/11/2018] [Indexed: 01/01/2023]
Abstract
Electron cryotomography (cryo-ET) is an imaging technique uniquely suited to the study of bacterial ultrastructure and cell biology. Recent years have seen a surge in structural and cell biology research on bacteria using cryo-ET. This research has driven major technical developments in the field, with applications emerging to address a wide range of biological questions. In this review, we explore the diversity of cryo-ET approaches used for structural and cellular microbiology, with a focus on in situ localization and structure determination of macromolecules. The first section describes strategies employed to locate target macromolecules within large cellular volumes. Next, we explore methods to study thick specimens by sample thinning. Finally, we review examples of macromolecular structure determination in a cellular context using cryo-ET. The examples outlined serve as powerful demonstrations of how the cellular location, structure, and function of any bacterial macromolecule of interest can be investigated using cryo-ET.
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Affiliation(s)
- Charlotte E Melia
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom
| | - Tanmay A M Bharat
- Sir William Dunn School of Pathology, University of Oxford, Oxford OX1 3RE, United Kingdom; Central Oxford Structural and Molecular Imaging Centre, University of Oxford, Oxford OX1 3RE, United Kingdom.
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131
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Cai S, Böck D, Pilhofer M, Gan L. The in situ structures of mono-, di-, and trinucleosomes in human heterochromatin. Mol Biol Cell 2018; 29:2450-2457. [PMID: 30091658 PMCID: PMC6233054 DOI: 10.1091/mbc.e18-05-0331] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The in situ three-dimensional organization of chromatin at the nucleosome and oligonucleosome levels is unknown. Here we use cryo-electron tomography to determine the in situ structures of HeLa nucleosomes, which have canonical core structures and asymmetric, flexible linker DNA. Subtomogram remapping suggests that sequential nucleosomes in heterochromatin follow irregular paths at the oligonucleosome level. This basic principle of higher-order repressive chromatin folding is compatible with the conformational variability of the two linker DNAs at the single-nucleosome level.
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Affiliation(s)
- Shujun Cai
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
| | - Désirée Böck
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Martin Pilhofer
- Institute of Molecular Biology and Biophysics, Eidgenössische Technische Hochschule Zürich, CH-8093 Zürich, Switzerland
| | - Lu Gan
- Department of Biological Sciences and Centre for BioImaging Sciences, National University of Singapore, Singapore 117543
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132
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Dillard RS, Hampton CM, Strauss JD, Ke Z, Altomara D, Guerrero-Ferreira RC, Kiss G, Wright ER. Biological Applications at the Cutting Edge of Cryo-Electron Microscopy. MICROSCOPY AND MICROANALYSIS : THE OFFICIAL JOURNAL OF MICROSCOPY SOCIETY OF AMERICA, MICROBEAM ANALYSIS SOCIETY, MICROSCOPICAL SOCIETY OF CANADA 2018; 24:406-419. [PMID: 30175702 PMCID: PMC6265046 DOI: 10.1017/s1431927618012382] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Cryo-electron microscopy (cryo-EM) is a powerful tool for macromolecular to near-atomic resolution structure determination in the biological sciences. The specimen is maintained in a near-native environment within a thin film of vitreous ice and imaged in a transmission electron microscope. The images can then be processed by a number of computational methods to produce three-dimensional information. Recent advances in sample preparation, imaging, and data processing have led to tremendous growth in the field of cryo-EM by providing higher resolution structures and the ability to investigate macromolecules within the context of the cell. Here, we review developments in sample preparation methods and substrates, detectors, phase plates, and cryo-correlative light and electron microscopy that have contributed to this expansion. We also have included specific biological applications.
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Affiliation(s)
- Rebecca S Dillard
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Cheri M Hampton
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Joshua D Strauss
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Zunlong Ke
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Deanna Altomara
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Ricardo C Guerrero-Ferreira
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Gabriella Kiss
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
| | - Elizabeth R Wright
- 1Division of Pediatric Infectious Diseases,Emory University School of Medicine,Children's Healthcare of Atlanta,Atlanta,GA 30322,USA
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134
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Robust workflow and instrumentation for cryo-focused ion beam milling of samples for electron cryotomography. Ultramicroscopy 2018; 190:1-11. [DOI: 10.1016/j.ultramic.2018.04.002] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 03/28/2018] [Accepted: 04/04/2018] [Indexed: 01/11/2023]
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135
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Medeiros JM, Böck D, Pilhofer M. Imaging bacteria inside their host by cryo-focused ion beam milling and electron cryotomography. Curr Opin Microbiol 2018; 43:62-68. [DOI: 10.1016/j.mib.2017.12.006] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Revised: 12/13/2017] [Accepted: 12/18/2017] [Indexed: 11/28/2022]
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136
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Golding I. Infection by bacteriophage lambda: an evolving paradigm for cellular individuality. Curr Opin Microbiol 2018; 43:9-13. [PMID: 29107897 PMCID: PMC5934347 DOI: 10.1016/j.mib.2017.09.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Revised: 09/14/2017] [Accepted: 09/25/2017] [Indexed: 12/19/2022]
Abstract
Since the earliest days of molecular biology, bacteriophage lambda has served to illuminate cellular function. Among its many roles, lambda infection is a paradigm for phenotypic heterogeneity among genetically identical cells. Early studies attributed this cellular individuality to random biochemical fluctuations, or 'noise'. More recently, however, attention has turned to the role played by deterministic hidden variables in driving single-cell behavior. Here, I briefly describe how studies in lambda are driving the shift in our understanding of cellular heterogeneity, allowing us to better appreciate the precision at which cells function.
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Affiliation(s)
- Ido Golding
- Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77005, USA.
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137
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Almeida GM, Leppänen M, Maasilta IJ, Sundberg LR. Bacteriophage imaging: past, present and future. Res Microbiol 2018; 169:488-494. [PMID: 29852217 DOI: 10.1016/j.resmic.2018.05.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 05/16/2018] [Accepted: 05/22/2018] [Indexed: 01/21/2023]
Abstract
The visualization of viral particles only became possible after the advent of the electron microscope. The first bacteriophage images were published in 1940 and were soon followed by many other publications that helped to elucidate the structure of the particles and their interaction with the bacterial hosts. As sample preparation improved and new technologies were developed, phage imaging became important approach to morphologically classify these viruses and helped to understand its importance in the biosphere. In this review we discuss the main milestones in phage imaging, how it affected our knowledge on these viruses and recent developments in the field.
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Affiliation(s)
- Gabriel Mf Almeida
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Survontie 9C, FI-40014, Jyväskylä, Finland.
| | - Miika Leppänen
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Survontie 9C, FI-40014, Jyväskylä, Finland; Department of Physics, Nanoscience Center, University of Jyväskylä, Survontie 9C, FI-40014, Jyväskylä, Finland.
| | - Ilari J Maasilta
- Department of Physics, Nanoscience Center, University of Jyväskylä, Survontie 9C, FI-40014, Jyväskylä, Finland.
| | - Lotta-Riina Sundberg
- Centre of Excellence in Biological Interactions, Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Survontie 9C, FI-40014, Jyväskylä, Finland.
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138
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Chaikeeratisak V, Nguyen K, Egan ME, Erb ML, Vavilina A, Pogliano J. The Phage Nucleus and Tubulin Spindle Are Conserved among Large Pseudomonas Phages. Cell Rep 2018; 20:1563-1571. [PMID: 28813669 DOI: 10.1016/j.celrep.2017.07.064] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2017] [Revised: 07/13/2017] [Accepted: 07/24/2017] [Indexed: 01/27/2023] Open
Abstract
We recently demonstrated that the large Pseudomonas chlororaphis bacteriophage 201φ2-1 assembles a nucleus-like structure that encloses phage DNA and segregates proteins according to function, with DNA processing proteins inside and metabolic enzymes and ribosomes outside the nucleus. Here, we investigate the replication pathway of the Pseudomonas aeruginosa bacteriophages φKZ and φPA3. Bacteriophages φKZ and φPA3 encode a proteinaceous shell that assembles a nucleus-like structure that compartmentalizes proteins and DNA during viral infection. We show that the tubulin-like protein PhuZ encoded by each phage assembles a bipolar spindle that displays dynamic instability and positions the nucleus at midcell. Our results suggest that the phage spindle and nucleus play the same functional role in all three phages, 201φ2-1, φKZ, and φPA3, demonstrating that these key structures are conserved among large Pseudomonas phages.
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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
| | - MacKennon E Egan
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Marcella L Erb
- 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
| | - Joe Pogliano
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA.
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139
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Erdmann PS, Plitzko JM, Baumeister W. Addressing cellular compartmentalization by in situ cryo-electron tomography. Curr Opin Colloid Interface Sci 2018. [DOI: 10.1016/j.cocis.2018.05.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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140
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Abrahão J, Silva L, Silva LS, Khalil JYB, Rodrigues R, Arantes T, Assis F, Boratto P, Andrade M, Kroon EG, Ribeiro B, Bergier I, Seligmann H, Ghigo E, Colson P, Levasseur A, Kroemer G, Raoult D, La Scola B. Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere. Nat Commun 2018; 9:749. [PMID: 29487281 PMCID: PMC5829246 DOI: 10.1038/s41467-018-03168-1] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/23/2018] [Indexed: 02/07/2023] Open
Abstract
Here we report the discovery of two Tupanvirus strains, the longest tailed Mimiviridae members isolated in amoebae. Their genomes are 1.44–1.51 Mb linear double-strand DNA coding for 1276–1425 predicted proteins. Tupanviruses share the same ancestors with mimivirus lineages and these giant viruses present the largest translational apparatus within the known virosphere, with up to 70 tRNA, 20 aaRS, 11 factors for all translation steps, and factors related to tRNA/mRNA maturation and ribosome protein modification. Moreover, two sequences with significant similarity to intronic regions of 18 S rRNA genes are encoded by the tupanviruses and highly expressed. In this translation-associated gene set, only the ribosome is lacking. At high multiplicity of infections, tupanvirus is also cytotoxic and causes a severe shutdown of ribosomal RNA and a progressive degradation of the nucleus in host and non-host cells. The analysis of tupanviruses constitutes a new step toward understanding the evolution of giant viruses. Giant viruses are the largest viruses of the known virosphere and their genetic analysis can provide insights into virus evolution. Here, the authors discover Tupanvirus, a unique giant virus that has an unusually long tail and contains the largest translational apparatus of the known virosphere.
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Affiliation(s)
- Jônatas Abrahão
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Lorena Silva
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Ludmila Santos Silva
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.,Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | | | - Rodrigo Rodrigues
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Thalita Arantes
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Felipe Assis
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Paulo Boratto
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Miguel Andrade
- Laboratório de Microscopia Eletrônica e Virologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, 70910-900, Brazil
| | - Erna Geessien Kroon
- Laboratório de Vírus, Instituto de Ciências Biológicas, Departamento de Microbiologia, Universidade Federal de Minas Gerais, Belo Horizonte, 31270-901, Brazil
| | - Bergmann Ribeiro
- Laboratório de Microscopia Eletrônica e Virologia, Departamento de Biologia Celular, Instituto de Ciências Biológicas, Universidade de Brasília, Asa Norte, Brasília, 70910-900, Brazil
| | - Ivan Bergier
- Lab. Biomass Conversion, Embrapa Pantanal, R. 21 de Setembro 1880, 79320-900, Corumbá/MS, Brazil
| | - Herve Seligmann
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Eric Ghigo
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Philippe Colson
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France
| | - Guido Kroemer
- Cell Biology and Metabolomics Platforms, Gustave Roussy Cancer Campus, Villejuif, 94805, France.,Equipe 11 labellisée Ligue Nationale contre le Cancer, Centre de Recherche des Cordeliers, Paris, 75006, France.,Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, 75654, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, 75015, France.,Université Pierre et Marie Curie, Paris, 75005, France.,Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, 75015, France.,Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, SE-171 76, Sweden
| | - Didier Raoult
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.
| | - Bernard La Scola
- MEPHI, APHM, IRD 198, Aix Marseille Univ, IHU-Méditerranee Infection, 19-21 Bd Jean Moulin, 13005, Marseille, France.
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141
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Seligmann H, Raoult D. Stem-Loop RNA Hairpins in Giant Viruses: Invading rRNA-Like Repeats and a Template Free RNA. Front Microbiol 2018; 9:101. [PMID: 29449833 PMCID: PMC5799277 DOI: 10.3389/fmicb.2018.00101] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 01/16/2018] [Indexed: 12/31/2022] Open
Abstract
We examine the hypothesis that de novo template-free RNAs still form spontaneously, as they did at the origins of life, invade modern genomes, contribute new genetic material. Previously, analyses of RNA secondary structures suggested that some RNAs resembling ancestral (t)RNAs formed recently de novo, other parasitic sequences cluster with rRNAs. Here positive control analyses of additional RNA secondary structures confirm ancestral and de novo statuses of RNA grouped according to secondary structure. Viroids with branched stems resemble de novo RNAs, rod-shaped viroids resemble rRNA secondary structures, independently of GC contents. 5' UTR leading regions of West Nile and Dengue flavivirid viruses resemble de novo and rRNA structures, respectively. An RNA homologous with Megavirus, Dengue and West Nile genomes, copperhead snake microsatellites and levant cotton repeats, not templated by Mimivirus' genome, persists throughout Mimivirus' infection. Its secondary structure clusters with candidate de novo RNAs. The saltatory phyletic distribution and secondary structure of Mimivirus' peculiar RNA suggest occasional template-free polymerization of this sequence, rather than noncanonical transcriptions (swinger polymerization, posttranscriptional editing).
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Affiliation(s)
- Hervé Seligmann
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR MEPHI, Aix-Marseille Université, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
| | - Didier Raoult
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR MEPHI, Aix-Marseille Université, IRD, Assistance Publique-Hôpitaux de Marseille, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France
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142
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Berliner AJ, Mochizuki T, Stedman KM. Astrovirology: Viruses at Large in the Universe. ASTROBIOLOGY 2018; 18:207-223. [PMID: 29319335 DOI: 10.1089/ast.2017.1649] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Viruses are the most abundant biological entities on modern Earth. They are highly diverse both in structure and genomic sequence, play critical roles in evolution, strongly influence terran biogeochemistry, and are believed to have played important roles in the origin and evolution of life. However, there is yet very little focus on viruses in astrobiology. Viruses arguably have coexisted with cellular life-forms since the earliest stages of life, may have been directly involved therein, and have profoundly influenced cellular evolution. Viruses are the only entities on modern Earth to use either RNA or DNA in both single- and double-stranded forms for their genetic material and thus may provide a model for the putative RNA-protein world. With this review, we hope to inspire integration of virus research into astrobiology and also point out pressing unanswered questions in astrovirology, particularly regarding the detection of virus biosignatures and whether viruses could be spread extraterrestrially. We present basic virology principles, an inclusive definition of viruses, review current virology research pertinent to astrobiology, and propose ideas for future astrovirology research foci. Key Words: Astrobiology-Virology-Biosignatures-Origin of life-Roadmap. Astrobiology 18, 207-223.
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Affiliation(s)
| | | | - Kenneth M Stedman
- 3 Center for Life in Extreme Environments and Biology Department, Portland State University , Oregon, USA
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143
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Wagstaff J, Löwe J. Prokaryotic cytoskeletons: protein filaments organizing small cells. Nat Rev Microbiol 2018; 16:187-201. [PMID: 29355854 DOI: 10.1038/nrmicro.2017.153] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Most, if not all, bacterial and archaeal cells contain at least one protein filament system. Although these filament systems in some cases form structures that are very similar to eukaryotic cytoskeletons, the term 'prokaryotic cytoskeletons' is used to refer to many different kinds of protein filaments. Cytoskeletons achieve their functions through polymerization of protein monomers and the resulting ability to access length scales larger than the size of the monomer. Prokaryotic cytoskeletons are involved in many fundamental aspects of prokaryotic cell biology and have important roles in cell shape determination, cell division and nonchromosomal DNA segregation. Some of the filament-forming proteins have been classified into a small number of conserved protein families, for example, the almost ubiquitous tubulin and actin superfamilies. To understand what makes filaments special and how the cytoskeletons they form enable cells to perform essential functions, the structure and function of cytoskeletal molecules and their filaments have been investigated in diverse bacteria and archaea. In this Review, we bring these data together to highlight the diverse ways that linear protein polymers can be used to organize other molecules and structures in bacteria and archaea.
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Affiliation(s)
- James Wagstaff
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
| | - Jan Löwe
- Medical Research Council Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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144
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145
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Serwer P, Wright ET, Demeler B, Jiang W. States of phage T3/T7 capsids: buoyant density centrifugation and cryo-EM. Biophys Rev 2017; 10:583-596. [PMID: 29243090 DOI: 10.1007/s12551-017-0372-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 11/20/2017] [Indexed: 12/16/2022] Open
Abstract
Mature double-stranded DNA bacteriophages have capsids with symmetrical shells that typically resist disruption, as they must to survive in the wild. However, flexibility and associated dynamism assist function. We describe biochemistry-oriented procedures used to find previously obscure flexibility for capsids of the related phages, T3 and T7. The primary procedures are hydration-based buoyant density ultracentrifugation and purified particle-based cryo-electron microscopy (cryo-EM). We review the buoyant density centrifugation in detail. The mature, stable T3/T7 capsid is a shell flexibility-derived conversion product of an initially assembled procapsid (capsid I). During DNA packaging, capsid I expands and loses a scaffolding protein to form capsid II. The following are observations made with capsid II. (1) The in vivo DNA packaging of wild type T3 generates capsid II that has a slight (1.4%), cryo-EM-detected hyper-expansion relative to the mature phage capsid. (2) DNA packaging in some altered conditions generates more extensive hyper-expansion of capsid II, initially detected by hydration-based preparative buoyant density centrifugation in Nycodenz density gradients. (3) Capsid contraction sometimes occurs, e.g., during quantized leakage of DNA from mature T3 capsids without a tail.
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Affiliation(s)
- Philip Serwer
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA.
| | - Elena T Wright
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Borries Demeler
- Department of Biochemistry and Structural Biology, The University of Texas Health Science Center, 7703 Floyd Curl Drive, San Antonio, TX, 78229-3900, USA
| | - Wen Jiang
- Markey Center for Structural Biology, Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
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146
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Baker LA, Sinnige T, Schellenberger P, de Keyzer J, Siebert CA, Driessen AJM, Baldus M, Grünewald K. Combined 1H-Detected Solid-State NMR Spectroscopy and Electron Cryotomography to Study Membrane Proteins across Resolutions in Native Environments. Structure 2017; 26:161-170.e3. [PMID: 29249608 PMCID: PMC5758107 DOI: 10.1016/j.str.2017.11.011] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2017] [Revised: 10/02/2017] [Accepted: 11/15/2017] [Indexed: 11/15/2022]
Abstract
Membrane proteins remain challenging targets for structural biology, despite much effort, as their native environment is heterogeneous and complex. Most methods rely on detergents to extract membrane proteins from their native environment, but this removal can significantly alter the structure and function of these proteins. Here, we overcome these challenges with a hybrid method to study membrane proteins in their native membranes, combining high-resolution solid-state nuclear magnetic resonance spectroscopy and electron cryotomography using the same sample. Our method allows the structure and function of membrane proteins to be studied in their native environments, across different spatial and temporal resolutions, and the combination is more powerful than each technique individually. We use the method to demonstrate that the bacterial membrane protein YidC adopts a different conformation in native membranes and that substrate binding to YidC in these native membranes differs from purified and reconstituted systems. CryoET and ssNMR give complementary information about proteins in native membranes One sample can be prepared for both methods without the use of detergents Hybrid method shows differences between purified and native preparations of YidC Sample preparation reduces costs and time and suggests new strategy for assignment
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Affiliation(s)
- Lindsay A Baker
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands; Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
| | - Tessa Sinnige
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands
| | - Pascale Schellenberger
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Jeanine de Keyzer
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 11, 9747 AG Groningen, the Netherlands
| | - C Alistair Siebert
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Arnold J M Driessen
- Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 7, 9747 AG Groningen, the Netherlands; The Zernike Institute for Advanced Materials, University of Groningen, Nijenborgh 11, 9747 AG Groningen, the Netherlands
| | - Marc Baldus
- NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, the Netherlands.
| | - Kay Grünewald
- Oxford Particle Imaging Centre, Division of Structural Biology, University of Oxford, The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.
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147
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Ali B, Desmond MI, Mallory SA, Benítez AD, Buckley LJ, Weintraub ST, Osier MV, Black LW, Thomas JA. To Be or Not To Be T4: Evidence of a Complex Evolutionary Pathway of Head Structure and Assembly in Giant Salmonella Virus SPN3US. Front Microbiol 2017; 8:2251. [PMID: 29187846 PMCID: PMC5694885 DOI: 10.3389/fmicb.2017.02251] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Accepted: 10/31/2017] [Indexed: 11/18/2022] Open
Abstract
Giant Salmonella phage SPN3US has a 240-kb dsDNA genome and a large complex virion composed of many proteins for which the functions of most are undefined. We recently determined that SPN3US shares a core set of genes with related giant phages and sequenced and characterized 18 amber mutants to facilitate its use as a genetic model system. Notably, SPN3US and related giant phages contain a bolus of ejection proteins within their heads, including a multi-subunit virion RNA polymerase (vRNAP), that enter the host cell with the DNA during infection. In this study, we characterized the SPN3US virion using mass spectrometry to gain insight into its head composition and the features that its head shares with those of related giant phages and with T4 phage. SPN3US has only homologs to the T4 proteins critical for prohead shell formation, the portal and major capsid proteins, as well as to the major enzymes essential for head maturation, the prohead protease and large terminase subunit. Eight of ~50 SPN3US head proteins were found to undergo proteolytic processing at a cleavage motif by the prohead protease gp245. Gp245 undergoes auto-cleavage of its C-terminus, suggesting this is a conserved activation and/or maturation feature of related phage proteases. Analyses of essential head gene mutants showed that the five subunits of the vRNAP must be assembled for any subunit to be incorporated into the prohead, although the assembled vRNAP must then undergo subsequent major conformational rearrangements in the DNA packed capsid to allow ejection through the ~30 Å diameter tail tube for transcription from the injected DNA. In addition, ejection protein candidate gp243 was found to play a critical role in head assembly. Our analyses of the vRNAP and gp243 mutants highlighted an unexpected dichotomy in giant phage head maturation: while all analyzed giant phages have a homologous protease that processes major capsid and portal proteins, processing of ejection proteins is not always a stable/defining feature. Our identification in SPN3US, and related phages, of a diverged paralog to the prohead protease further hints toward a complicated evolutionary pathway for giant phage head structure and assembly.
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Affiliation(s)
- Bazla Ali
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Maxim I Desmond
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Sara A Mallory
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Andrea D Benítez
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Larry J Buckley
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Susan T Weintraub
- Biochemistry, University of Texas Health Science Center at San Antonio, San Antonio, TX, United States
| | - Michael V Osier
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
| | - Lindsay W Black
- University of Maryland School of Medicine, Baltimore, MD, United States
| | - Julie A Thomas
- Thomas H. Gosnell School of Life Sciences, Rochester Institute of Technology, Rochester, NY, United States
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148
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Wagner J, Schaffer M, Fernández-Busnadiego R. Cryo-electron tomography-the cell biology that came in from the cold. FEBS Lett 2017; 591:2520-2533. [PMID: 28726246 DOI: 10.1002/1873-3468.12757] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Revised: 06/26/2017] [Accepted: 07/14/2017] [Indexed: 12/27/2022]
Abstract
Cryo-electron tomography (cryo-ET) provides high-resolution 3D views into cells pristinely preserved by vitrification. Recent technical advances such as direct electron detectors, the Volta phase plate and cryo-focused ion beam milling have dramatically pushed image quality and expanded the range of cryo-ET applications. Cryo-ET not only allows mapping the positions and interactions of macromolecules within their intact cellular context, but can also reveal their in situ structure at increasing resolution. Here, we review how recent work using cutting-edge cryo-ET technologies is starting to provide fresh views into different aspects of cellular biology at an unprecedented level of detail. We anticipate that these developments will soon make cryo-ET a fundamental technique in cell biology.
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149
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150
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Formation of a Viral Replication Focus in Sulfolobus Cells Infected by the Rudivirus Sulfolobus islandicus Rod-Shaped Virus 2. J Virol 2017; 91:JVI.00486-17. [PMID: 28424282 DOI: 10.1128/jvi.00486-17] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 04/11/2017] [Indexed: 01/05/2023] Open
Abstract
Viral factories are compartmentalized centers for viral replication and assembly in infected eukaryotic cells. Here, we report the formation of a replication focus by prototypical archaeal Sulfolobus islandicus rod-shaped virus 2 (SIRV2) in the model archaeon Sulfolobus This rod-shaped virus belongs to the viral family Rudiviridae, carrying linear double-stranded DNA (dsDNA) genomes, which are very common in geothermal environments. We demonstrate that SIRV2 DNA synthesis is confined to a focus near the periphery of infected cells. Moreover, viral and cellular replication proteins are recruited to, and concentrated in, the viral replication focus. Furthermore, we show that of the four host DNA polymerases (DNA polymerase I [Dpo1] to Dpo4), only Dpo1 participates in viral DNA synthesis. This constitutes the first report of the formation of a viral replication focus in archaeal cells, suggesting that organization of viral replication in foci is a widespread strategy employed by viruses of the three domains of life.IMPORTANCE The organization of viral replication in foci or viral factories has been mostly described for different eukaryotic viruses and for several bacteriophages. This work constitutes the first report of the formation of a viral replication center by a virus infecting members of the Archaea domain.
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