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Washington JM, Basta H, De Jesus AB, Bendele MG, Cresawn SG, Ginser EK. Expanding the Diversity of Actinobacterial Tectiviridae: A Novel Genus from Microbacterium. Viruses 2025; 17:113. [PMID: 39861902 PMCID: PMC11768872 DOI: 10.3390/v17010113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2024] [Revised: 01/11/2025] [Accepted: 01/12/2025] [Indexed: 01/27/2025] Open
Abstract
Six novel Microbacterium phages belonging to the Tectiviridae family were isolated using Microbacterium testaceum as a host. Phages MuffinTheCat, Badulia, DesireeRose, Bee17, SCoupsA, and LuzDeMundo were purified from environmental samples by students participating in the Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) program at Alliance University, New York. The phages have linear dsDNA genomes 15,438-15,636 bp with 112-120 bp inverted terminal repeats. Transmission electron microscopy (TEM) imaging analysis revealed that the six novel phages have six-sided icosahedral double-layered capsids with an internal lipid membrane that occasionally forms protruding nanotubules. Annotation analysis determined that the novel Microbacterium phages all have 32-34 protein-coding genes and no tRNAs. Like other Tectiviridae, the phage genomes are arranged into two segments and include three highly conserved family genes that encode a DNA polymerase, double jelly-roll major capsid protein, and packaging ATPase. Although the novel bacteriophages have 91.6 to 97.5% nucleotide sequence similarity to each other, they are at most 58% similar to previously characterized Tectiviridae genera. Consequently, these novel Microbacterium phages expand the diversity of the Tectiviridae family, and we propose they form the sixth genus, Zetatectivirus.
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Affiliation(s)
- Jacqueline M. Washington
- Department of Biology and Chemistry, Alliance University, New York, NY 10004, USA;
- Department of Biology, Empire State University, Saratoga Springs, NY 12866, USA
| | - Holly Basta
- Department of Biology, Rocky Mountain College, Billings, MT 59102, USA;
| | - Angela Bryanne De Jesus
- Department of Biology and Chemistry, Alliance University, New York, NY 10004, USA;
- Weil Cornell Medicine, New York, NY 10021, USA
| | - Madison G. Bendele
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA; (M.G.B.); (S.G.C.)
| | - Steven G. Cresawn
- Department of Biology, James Madison University, Harrisonburg, VA 22807, USA; (M.G.B.); (S.G.C.)
| | - Emily K. Ginser
- Biological Sciences Department, University of Pittsburgh, Pittsburgh, PA 15260, USA;
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2
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Zhou Q, Lok SM. Visualizing the virus world inside the cell by cryo-electron tomography. J Virol 2024; 98:e0108523. [PMID: 39494908 PMCID: PMC11650999 DOI: 10.1128/jvi.01085-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2024] Open
Abstract
Structural studies on purified virus have revealed intricate architectures, but there is little structural information on how viruses interact with host cells in situ. Cryo-focused ion beam (FIB) milling and cryo-electron tomography (cryo-ET) have emerged as revolutionary tools in structural biology to visualize the dynamic conformational of viral particles and their interactions with host factors within infected cells. Here, we review the state-of-the-art cryo-ET technique for in situ viral structure studies and highlight exemplary studies that showcase the remarkable capabilities of cryo-ET in capturing the dynamic virus-host interaction, advancing our understanding of viral infection and pathogenesis.
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Affiliation(s)
- Qunfei Zhou
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
| | - Shee-Mei Lok
- Program in Emerging Infectious Diseases, Duke-National University of Singapore Medical School, Singapore, Singapore
- Department of Biological Sciences, Centre for BioImaging Sciences, National University of Singapore, Singapore, Singapore
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3
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Thung TY, Hall A, Jati AP, White ME, Bamert RS, Tan KS, Press C, Taiaroa G, Short FL, Dunstan RA, Lithgow T. Genetic variation in individuals from a population of the minimalist bacteriophage Merri-merri-uth nyilam marra-natj driving evolution of the virus. mBio 2024; 15:e0256424. [PMID: 39475328 PMCID: PMC11633184 DOI: 10.1128/mbio.02564-24] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2024] [Accepted: 09/30/2024] [Indexed: 12/12/2024] Open
Abstract
In a survey of a waterway on Wurundjeri land, two sub-populations of the bacteriophage Merri-merri-uth nyilam marra-natj (phage MMNM) were isolated on a permissive host, Klebsiella B5055 of capsule-type K2, but were distinguished by minor phenotypic differences. The variant phage MMNM(Ala134) showed an inhibited activity against Klebsiella AJ174-2, and this was used as a basis to select for further variation through experimental evolution. Over the course of an evolution experiment, 20 phages that evolved distinct phenotypes in terms of the morphologies of plaques formed when they infected host Klebsiella were subject to whole-genome sequencing. The evolved phages had mutations in a small set of proteins that contribute to the baseplate portion of the phage virion. Phages MMNM and MMNM(Ala134) are minimalist phages, with baseplates formed from only five predicted subunits, akin to other minimalist phages Pam3 and XM1. The homology between all three minimalist phages provided a structural framework to interpret the two classes of mutations derived through evolution in the presence of the semi-permissive host: those that affect the interfacial surfaces between baseplate subunits, and those in a base-plate associated tail-fiber. This study evidences that multiple small mutations can be fixed into a sub-population of phage to provide a basis for phenotypic variation that we suggest could ultimately provide for a shift of virus properties, as an alternative evolutionary scenario to the major genetic events that result in more well-studied evolutionary mechanism of phage mosaicism. IMPORTANCE Bacteriophages (phages) are viruses that prey on bacteria. This study sampled natural phage populations to test the hypothesis that untapped genetic variation within a population can be the basis for the selection of phages to diversify their host-range. Sampling of a freshwater site revealed two populations of the phage Merri-merri-uth nyilam marra-natj (phage MMNM), differing by a variant residue (Val134Ala) in the baseplate protein MMNM_26. This sequence variation modulated bacterial killing in plaques, and further evolution of the phages on a semi-permissive bacterial host led to a new generation of phages with more diverse phenotypes in killing the bacterium Klebsiella pneumoniae.
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Affiliation(s)
- Tze Y. Thung
- Center to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Alex Hall
- Center to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Afif P. Jati
- Center to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Murray E. White
- Center to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Rebecca S. Bamert
- Center to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Kher Shing Tan
- Center to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Cara Press
- Center to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - George Taiaroa
- Department of Microbiology and Immunology, The Peter Doherty Institute, The University of Melbourne, Parkville, Australia
| | - Francesca L. Short
- Center to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Rhys A. Dunstan
- Center to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
| | - Trevor Lithgow
- Center to Impact AMR, Monash University, Clayton, Australia
- Infection Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Australia
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4
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Evseev P, Gutnik D, Evpak A, Kasimova A, Miroshnikov K. Origin, Evolution and Diversity of φ29-like Phages-Review and Bioinformatic Analysis. Int J Mol Sci 2024; 25:10838. [PMID: 39409167 PMCID: PMC11476376 DOI: 10.3390/ijms251910838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2024] [Revised: 10/04/2024] [Accepted: 10/07/2024] [Indexed: 10/20/2024] Open
Abstract
Phage φ29 and related bacteriophages are currently the smallest known tailed viruses infecting various representatives of both Gram-positive and Gram-negative bacteria. They are characterised by genomic content features and distinctive properties that are unique among known tailed phages; their characteristics include protein primer-driven replication and a packaging process characteristic of this group. Searches conducted using public genomic databases revealed in excess of 2000 entries, including bacteriophages, phage plasmids and sequences identified as being archaeal that share the characteristic features of phage φ29. An analysis of predicted proteins, however, indicated that the metagenomic sequences attributed as archaeal appear to be misclassified and belong to bacteriophages. An analysis of the translated polypeptides of major capsid proteins (MCPs) of φ29-related phages indicated the dissimilarity of MCP sequences to those of almost all other known Caudoviricetes groups and a possible distant relationship to MCPs of T7-like (Autographiviridae) phages. Sequence searches conducted using HMM revealed the relatedness between the main structural proteins of φ29-like phages and an unusual lactococcal phage, KSY1 (Chopinvirus KSY1), whose genome contains two genes of RNA polymerase that are similar to the RNA polymerases of phages of the Autographiviridae and Schitoviridae (N4-like) families. An analysis of the tail tube proteins of φ29-like phages indicated their dissimilarity of the lower collar protein to tail proteins of all other viral groups, but revealed its possible distant relatedness with proteins of toxin translocation complexes. The combination of the unique features and distinctive origin of φ29-related phages suggests the categorisation of this vast group in a new order or as a new taxon of a higher rank.
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Affiliation(s)
- Peter Evseev
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, 117997 Moscow, Russia
- Laboratory of Molecular Microbiology, Pirogov Russian National Research Medical University, Ostrovityanova Street 1, 117997 Moscow, Russia
| | - Daria Gutnik
- Limnological Institute, Siberian Branch of the Russian Academy of Sciences, Ulan-Batorsakaya Street, 3, 664033 Irkutsk, Russia
| | - Alena Evpak
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, 117997 Moscow, Russia
| | - Anastasia Kasimova
- Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt, 47, 119991 Moscow, Russia
| | - Konstantin Miroshnikov
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Miklukho-Maklaya Street 16/10, 117997 Moscow, Russia
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5
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Stanton CR, Petrovski S, Batinovic S. Isolation of a PRD1-like phage uncovers the carriage of three putative conjugative plasmids in clinical Burkholderia contaminans. Res Microbiol 2024; 175:104202. [PMID: 38582389 DOI: 10.1016/j.resmic.2024.104202] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Revised: 03/27/2024] [Accepted: 03/27/2024] [Indexed: 04/08/2024]
Abstract
The Burkholderia cepacia complex (Bcc) is a group of increasingly multi-drug resistant opportunistic bacteria. This resistance is driven through a combination of intrinsic factors and the carriage of a broad range of conjugative plasmids harbouring virulence determinants. Therefore, novel treatments are required to treat and prevent further spread of these virulence determinants. In the search for phages infective for clinical Bcc isolates, CSP1 phage, a PRD1-like phage was isolated. CSP1 phage was found to require pilus machinery commonly encoded on conjugative plasmids to facilitate infection of Gram-negative bacteria genera including Escherichia and Pseudomonas. Whole genome sequencing and characterisation of one of the clinical Burkholderia isolates revealed it to be Burkholderia contaminans. B. contaminans 5080 was found to contain a genome of over 8 Mbp encoding multiple intrinsic resistance factors, such as efflux pump systems, but more interestingly, carried three novel plasmids encoding multiple putative virulence factors for increased host fitness, including antimicrobial resistance. Even though PRD1-like phages are broad host range, their use in novel antimicrobial treatments shouldn't be dismissed, as the dissemination potential of conjugative plasmids is extensive. Continued survey of clinical bacterial strains is also key to understanding the spread of antimicrobial resistance determinants and plasmid evolution.
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Affiliation(s)
- Cassandra R Stanton
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Victoria, Australia
| | - Steve Petrovski
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Victoria, Australia.
| | - Steven Batinovic
- Department of Microbiology, Anatomy, Physiology and Pharmacology, La Trobe University, Bundoora, Victoria, Australia; Division of Materials Science and Chemical Engineering, Yokohama National University, Yokohama, Kanagawa, Japan
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6
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Wang Z, Yang X, Wang H, Wang S, Fang R, Li X, Xing J, Wu Q, Li Z, Song N. Characterization and efficacy against carbapenem-resistant Acinetobacter baumannii of a novel Friunavirus phage from sewage. Front Cell Infect Microbiol 2024; 14:1382145. [PMID: 38736748 PMCID: PMC11086170 DOI: 10.3389/fcimb.2024.1382145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Accepted: 04/08/2024] [Indexed: 05/14/2024] Open
Abstract
Carbapenem-resistant Acinetobacter baumannii (CRAB) has become a new threat in recent years, owing to its rapidly increasing resistance to antibiotics and new effective therapies are needed to combat this pathogen. Phage therapy is considered to be the most promising alternative for treating CRAB infections. In this study, a novel phage, Ab_WF01, which can lyse clinical CRAB, was isolated and characterized from hospital sewage. The multiplicity of infection, morphology, one-step growth curve, stability, sensitivity, and lytic activity of the phage were also investigated. The genome of phage Ab_WF01 was 41, 317 bp in size with a GC content of 39.12% and encoded 51 open reading frames (ORFs). tRNA, virulence, and antibiotic resistance genes were not detected in the phage genome. Comparative genomic and phylogenetic analyses suggest that phage Ab_WF01 is a novel species of the genus Friunavirus, subfamily Beijerinckvirinae, and family Autographiviridae. The in vivo results showed that phage Ab_WF01 significantly increased the survival rate of CRAB-infected Galleria mellonella (from 0% to 70% at 48 h) and mice (from 0% to 60% for 7 days). Moreover, after day 3 post-infection, phage Ab_WF01 reduced inflammatory response, with strongly ameliorated histological damage and bacterial clearance in infected tissue organs (lungs, liver, and spleen) in mouse CRAB infection model. Taken together, these results show that phage Ab_WF01 holds great promise as a potential alternative agent with excellent stability for against CRAB infections.
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Affiliation(s)
- Zhitao Wang
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Xue Yang
- School of Pharmacy, Shandong Second Medical University, Weifang, China
| | - Hui Wang
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Shuxian Wang
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Ren Fang
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Xiaotian Li
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Jiayin Xing
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
| | - Qianqian Wu
- Department of Clinical Laboratory, Affiliated Hospital of Shandong Second Medical University, Weifang, China
| | - Zhaoli Li
- SAFE Pharmaceutical Technology Co. Ltd., Beijing, China
| | - Ningning Song
- Weifang Key Laboratory of Respiratory Tract Pathogens and Drug Therapy, School of Life Science and Technology, Shandong Second Medical University, Weifang, China
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7
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Ebrahim T, Ebrahim AS, Kandouz M. Diversity of Intercellular Communication Modes: A Cancer Biology Perspective. Cells 2024; 13:495. [PMID: 38534339 PMCID: PMC10969453 DOI: 10.3390/cells13060495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/27/2024] [Accepted: 03/10/2024] [Indexed: 03/28/2024] Open
Abstract
From the moment a cell is on the path to malignant transformation, its interaction with other cells from the microenvironment becomes altered. The flow of molecular information is at the heart of the cellular and systemic fate in tumors, and various processes participate in conveying key molecular information from or to certain cancer cells. For instance, the loss of tight junction molecules is part of the signal sent to cancer cells so that they are no longer bound to the primary tumors and are thus free to travel and metastasize. Upon the targeting of a single cell by a therapeutic drug, gap junctions are able to communicate death information to by-standing cells. The discovery of the importance of novel modes of cell-cell communication such as different types of extracellular vesicles or tunneling nanotubes is changing the way scientists look at these processes. However, are they all actively involved in different contexts at the same time or are they recruited to fulfill specific tasks? What does the multiplicity of modes mean for the overall progression of the disease? Here, we extend an open invitation to think about the overall significance of these questions, rather than engage in an elusive attempt at a systematic repertory of the mechanisms at play.
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Affiliation(s)
- Thanzeela Ebrahim
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Abdul Shukkur Ebrahim
- Department of Ophthalmology, Visual and Anatomical Sciences, Wayne State University School of Medicine, Detroit, MI 48202, USA
| | - Mustapha Kandouz
- Department of Pathology, Wayne State University School of Medicine, Detroit, MI 48202, USA
- Karmanos Cancer Institute, Wayne State University School of Medicine, Detroit, MI 48202, USA
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8
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Koonin EV, Kuhn JH, Dolja VV, Krupovic M. Megataxonomy and global ecology of the virosphere. THE ISME JOURNAL 2024; 18:wrad042. [PMID: 38365236 PMCID: PMC10848233 DOI: 10.1093/ismejo/wrad042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 12/22/2023] [Accepted: 12/28/2023] [Indexed: 02/18/2024]
Abstract
Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.
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Affiliation(s)
- Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, United States
| | - Jens H Kuhn
- Integrated Research Facility at Fort Detrick, Division of Clinical Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Fort Detrick, Frederick, MD 21702, United States
| | - Valerian V Dolja
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331, United States
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, Archaeal Virology Unit, 75015 Paris, France
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9
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Kuiper BP, Schöntag AMC, Oksanen HM, Daum B, Quax TEF. Archaeal virus entry and egress. MICROLIFE 2024; 5:uqad048. [PMID: 38234448 PMCID: PMC10791045 DOI: 10.1093/femsml/uqad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/20/2023] [Revised: 11/08/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these viruses enter and exit their host cells. Research on archaeal viruses has lately made significant progress due to advances in genetic tools and imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, a steady output of newly identified archaeal viral receptors and egress mechanisms has offered the first insight into how archaeal viruses interact with the archaeal cell envelope. As more details about archaeal viral entry and egress are unravelled, patterns are starting to emerge. This helps to better understand the interactions between viruses and the archaeal cell envelope and how these compare to infection strategies of viruses in other domains of life. Here, we provide an overview of recent developments in the field of archaeal viral entry and egress, shedding light onto the most elusive part of the virosphere.
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Affiliation(s)
- Bastiaan P Kuiper
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Anna M C Schöntag
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Viikinkaari 9, FI-00014 Helsinki, Finland
| | - Bertram Daum
- Living Systems Institute, Faculty of Health and Life Sciences, University of Exeter, Exeter EX4 4QD, United Kingdom
| | - Tessa E F Quax
- Biology of Archaea and Viruses, Department of Molecular Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, Faculty for Science and Engineering, University of Groningen, 7th floor, Nijenborgh 7, 9747 AG Groningen, the Netherlands
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10
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van Raaij MJ. Bacteriophage Receptor Recognition and Nucleic Acid Transfer. Subcell Biochem 2024; 105:593-628. [PMID: 39738959 DOI: 10.1007/978-3-031-65187-8_17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2025]
Abstract
Correct host cell recognition is important in the replication cycle for any virus, including bacterial viruses. This essential step should occur before the bacteriophage commits to transferring its genomic material into the target bacterium. In this chapter, we will discuss the mechanisms and proteins bacteriophages use for receptor recognition (just before full commitment to infection) and nucleic acid injection, which occurs just after commitment. Some bacteriophages use proteins of the capsid proper for host cell recognition, others use specialised spikes or fibres. Usually, several identical recognition events take place, and the information that a suitable host cell has been encountered is somehow transferred to the part of the bacteriophage capsid involved in nucleic acid transfer. The main part of the capsids of bacteriophages stays on the cell surface after transferring their genome, although a few specialised proteins move with the DNA, either forming a conduit, protecting the nucleic acids after transfer and/or functioning in the process of transcription and translation.
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Affiliation(s)
- Mark J van Raaij
- Department of Macromolecular Structure, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain.
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11
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Stuart DI, Oksanen HM, Abrescia NGA. Integrative Approaches to Study Virus Structures. Subcell Biochem 2024; 105:247-297. [PMID: 39738949 DOI: 10.1007/978-3-031-65187-8_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2025]
Abstract
A virus particle must work as a strongroom to protect its genome, but at the same time it must undergo dramatic conformational changes to infect the cell in order to replicate and assemble progeny. Thus, viruses are miniaturized wonders whose structural complexity requires investigation by a combination of different techniques that can tackle both static and dynamic processes. In this chapter, we will illustrate how major structural techniques such as X-ray crystallography and electron microscopy can be combined with other techniques to determine the structure of complex viruses. The power of these hybrid approaches is discussed through a number of examples.
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Affiliation(s)
- David I Stuart
- Division of Structural Biology, The Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
- Diamond Light Source Ltd, Diamond House, Harwell Science and Innovation Campus, Didcot, UK
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, CIC bioGUNE - Basque Research and Technology Alliance, Derio, Spain.
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain.
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12
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Bárdy P, MacDonald CI, Pantůček R, Antson AA, Fogg PC. Jorvik: A membrane-containing phage that will likely found a new family within Vinavirales. iScience 2023; 26:108104. [PMID: 37867962 PMCID: PMC10589892 DOI: 10.1016/j.isci.2023.108104] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 07/23/2023] [Accepted: 09/27/2023] [Indexed: 10/24/2023] Open
Abstract
Although membrane-containing dsDNA bacterial viruses are some of the most prevalent predators in aquatic environments, we know little about how they function due to their intractability in the laboratory. Here, we have identified and thoroughly characterized a new type of membrane-containing bacteriophage, Jorvik, that infects the freshwater mixotrophic model bacterium Rhodobacter capsulatus. Jorvik is extremely virulent, can persist in the host integrated into the RuBisCo operon and encodes two experimentally verified cell wall hydrolases. Jorvik-like prophages are abundant in the genomes of Alphaproteobacteria, are distantly related to known viruses of the class Tectiliviricetes, and we propose they should be classified as a new family. Crucially, we demonstrate how widely used phage manipulation methods should be adjusted to prevent loss of virus infectivity. Our thorough characterization of environmental phage Jorvik provides important experimental insights about phage diversity and interactions in microbial communities that are often unexplored in common metagenomic analyses.
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Affiliation(s)
- Pavol Bárdy
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Conor I.W. MacDonald
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
| | - Roman Pantůček
- Department of Experimental Biology, Faculty of Science, Masaryk University, 625 00 Brno, Czech Republic
| | - Alfred A. Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5NG, UK
| | - Paul C.M. Fogg
- York Biomedical Research Institute, University of York, Wentworth Way, York YO10 5NG, UK
- Biology Department, University of York, Wentworth Way, York YO10 5DD, UK
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13
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Inline-tandem purification of viruses from cell lysate by agarose-based chromatography. J Chromatogr B Analyt Technol Biomed Life Sci 2022; 1192:123140. [DOI: 10.1016/j.jchromb.2022.123140] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 01/20/2022] [Accepted: 01/24/2022] [Indexed: 12/15/2022]
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14
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Duyvesteyn HME, Santos-Pérez I, Peccati F, Martinez-Castillo A, Walter TS, Reguera D, Goñi FM, Jiménez-Osés G, Oksanen HM, Stuart DI, Abrescia NGA. Bacteriophage PRD1 as a nanoscaffold for drug loading. NANOSCALE 2021; 13:19875-19883. [PMID: 34851350 PMCID: PMC8667075 DOI: 10.1039/d1nr04153c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/27/2021] [Accepted: 11/06/2021] [Indexed: 06/13/2023]
Abstract
Viruses are very attractive biomaterials owing to their capability as nanocarriers of genetic material. Efforts have been made to functionalize self-assembling viral protein capsids on their exterior or interior to selectively take up different payloads. PRD1 is a double-stranded DNA bacteriophage comprising an icosahedral protein outer capsid and an inner lipidic vesicle. Here, we report the three-dimensional structure of PRD1 in complex with the antipsychotic drug chlorpromazine (CPZ) by cryo-electron microscopy. We show that the jellyrolls of the viral major capsid protein P3, protruding outwards from the capsid shell, serve as scaffolds for loading heterocyclic CPZ molecules. Additional X-ray studies and molecular dynamics simulations show the binding modes and organization of CPZ molecules when complexed with P3 only and onto the virion surface. Collectively, we provide a proof of concept for the possible use of the lattice-like organisation and the quasi-symmetric morphology of virus capsomers for loading heterocyclic drugs with defined properties.
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Affiliation(s)
- Helen M E Duyvesteyn
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
| | - Isaac Santos-Pérez
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.
| | - Francesca Peccati
- Computational Chemistry Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
| | - Ane Martinez-Castillo
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.
| | - Thomas S Walter
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.
| | - David Reguera
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain
| | - Felix M Goñi
- Departamento de Bioquímica, University of the Basque Country (UPV/EHU) and Instituto Biofisika (CSIC, UPV/EHU), Leioa, Spain
| | - Gonzalo Jiménez-Osés
- Computational Chemistry Lab, CIC bioGUNE, Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - David I Stuart
- Division of Structural Biology, University of Oxford, The Henry Wellcome Building for Genomic Medicine, Headington, Oxford, UK.
- Diamond Light Source, Harwell Science and Innovation Campus, Didcot, UK
- Instruct-ERIC, Oxford House, Parkway Court, John Smith Drive, Oxford, UK
| | - Nicola G A Abrescia
- Structure and Cell Biology of Viruses Lab, Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Derio, Spain.
- IKERBASQUE, Basque Foundation for Science, Bilbao, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Instituto de Salud Carlos III, Madrid, Spain
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15
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Kalargyrou AA, Basche M, Hare A, West EL, Smith AJ, Ali RR, Pearson RA. Nanotube-like processes facilitate material transfer between photoreceptors. EMBO Rep 2021; 22:e53732. [PMID: 34494703 PMCID: PMC8567251 DOI: 10.15252/embr.202153732] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 12/12/2022] Open
Abstract
Neuronal communication is typically mediated via synapses and gap junctions. New forms of intercellular communication, including nanotubes (NTs) and extracellular vesicles (EVs), have been described for non-neuronal cells, but their role in neuronal communication is not known. Recently, transfer of cytoplasmic material between donor and host neurons ("material transfer") was shown to occur after photoreceptor transplantation. The cellular mechanism(s) underlying this surprising finding are unknown. Here, using transplantation, primary neuronal cultures and the generation of chimeric retinae, we show for the first time that mammalian photoreceptor neurons can form open-end NT-like processes. These processes permit the transfer of cytoplasmic and membrane-bound molecules in culture and after transplantation and can mediate gain-of-function in the acceptor cells. Rarely, organelles were also observed to transfer. Strikingly, use of chimeric retinae revealed that material transfer can occur between photoreceptors in the intact adult retina. Conversely, while photoreceptors are capable of releasing EVs, at least in culture, these are taken up by glia and not by retinal neurons. Our findings provide the first evidence of functional NT-like processes forming between sensory neurons in culture and in vivo.
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Affiliation(s)
- Aikaterini A Kalargyrou
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
| | - Mark Basche
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
| | - Aura Hare
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
| | - Emma L West
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
| | - Alexander J Smith
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
| | - Robin R Ali
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
- Kellogg Eye CenterUniversity of MichiganAnn ArborMIUSA
| | - Rachael A Pearson
- University College London Institute of OphthalmologyLondonUK
- Centre for Cell and Gene TherapyKing’s College LondonGuy’s HospitalLondonUK
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16
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Assisted assembly of bacteriophage T7 core components for genome translocation across the bacterial envelope. Proc Natl Acad Sci U S A 2021; 118:2026719118. [PMID: 34417311 DOI: 10.1073/pnas.2026719118] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In most bacteriophages, genome transport across bacterial envelopes is carried out by the tail machinery. In viruses of the Podoviridae family, in which the tail is not long enough to traverse the bacterial wall, it has been postulated that viral core proteins assembled inside the viral head are translocated and reassembled into a tube within the periplasm that extends the tail channel. Bacteriophage T7 infects Escherichia coli, and despite extensive studies, the precise mechanism by which its genome is translocated remains unknown. Using cryo-electron microscopy, we have resolved the structure of two different assemblies of the T7 DNA translocation complex composed of the core proteins gp15 and gp16. Gp15 alone forms a partially folded hexamer, which is further assembled upon interaction with gp16 into a tubular structure, forming a channel that could allow DNA passage. The structure of the gp15-gp16 complex also shows the location within gp16 of a canonical transglycosylase motif involved in the degradation of the bacterial peptidoglycan layer. This complex docks well in the tail extension structure found in the periplasm of T7-infected bacteria and matches the sixfold symmetry of the phage tail. In such cases, gp15 and gp16 that are initially present in the T7 capsid eightfold-symmetric core would change their oligomeric state upon reassembly in the periplasm. Altogether, these results allow us to propose a model for the assembly of the core translocation complex in the periplasm, which furthers understanding of the molecular mechanism involved in the release of T7 viral DNA into the bacterial cytoplasm.
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17
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Gillis A, Hock L, Mahillon J. Comparative Genomics of Prophages Sato and Sole Expands the Genetic Diversity Found in the Genus Betatectivirus. Microorganisms 2021; 9:1335. [PMID: 34205474 PMCID: PMC8234876 DOI: 10.3390/microorganisms9061335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/13/2021] [Accepted: 06/15/2021] [Indexed: 11/16/2022] Open
Abstract
Tectiviruses infecting the Bacillus cereus group represent part of the bacterial "plasmid repertoire" as they behave as linear plasmids during their lysogenic cycle. Several novel tectiviruses have been recently found infecting diverse strains belonging the B. cereus lineage. Here, we report and analyze the complete genome sequences of phages Sato and Sole. The linear dsDNA genome of Sato spans 14,852 bp with 32 coding DNA sequences (CDSs), whereas the one of Sole has 14,444 bp comprising 30 CDSs. Both phage genomes contain inverted terminal repeats and no tRNAs. Genomic comparisons and phylogenetic analyses placed these two phages within the genus Betatectivirus in the family Tectiviridae. Additional comparative genomic analyses indicated that the "gene regulation-genome replication" module of phages Sato and Sole is more diverse than previously observed among other fully sequenced betatectiviruses, displaying very low sequence similarities and containing some ORFans. Interestingly, the ssDNA binding protein encoded in this genomic module in phages Sato and Sole has very little amino acid similarity with those of reference betatectiviruses. Phylogenetic analyses showed that both Sato and Sole represent novel tectivirus species, thus we propose to include them as two novel species in the genus Betatectivirus.
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Affiliation(s)
- Annika Gillis
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Croix du Sud 2, L7.05.12, B-1348 Louvain-la-Neuve, Belgium;
| | | | - Jacques Mahillon
- Laboratory of Food and Environmental Microbiology, Earth and Life Institute, UCLouvain, Croix du Sud 2, L7.05.12, B-1348 Louvain-la-Neuve, Belgium;
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18
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A persistent giant algal virus, with a unique morphology, encodes an unprecedented number of genes involved in energy metabolism. J Virol 2021; 95:JVI.02446-20. [PMID: 33536167 PMCID: PMC8103676 DOI: 10.1128/jvi.02446-20] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Viruses have long been viewed as entities possessing extremely limited metabolic capacities. Over the last decade, however, this view has been challenged, as metabolic genes have been identified in viruses possessing large genomes and virions-the synthesis of which is energetically demanding. Here, we unveil peculiar phenotypic and genomic features of Prymnesium kappa virus RF01 (PkV RF01), a giant virus of the Mimiviridae family. We found that this virus encodes an unprecedented number of proteins involved in energy metabolism, such as all four succinate dehydrogenase (SDH) subunits (A-D) as well as key enzymes in the β-oxidation pathway. The SDHA gene was transcribed upon infection, indicating that the viral SDH is actively used by the virus- potentially to modulate its host's energy metabolism. We detected orthologous SDHA and SDHB genes in numerous genome fragments from uncultivated marine Mimiviridae viruses, which suggests that the viral SDH is widespread in oceans. PkV RF01 was less virulent compared with other cultured prymnesioviruses, a phenomenon possibly linked to the metabolic capacity of this virus and suggestive of relatively long co-evolution with its hosts. It also has a unique morphology, compared to other characterized viruses in the Mimiviridae family. Finally, we found that PkV RF01 is the only alga-infecting Mimiviridae virus encoding two aminoacyl-tRNA synthetases and enzymes corresponding to an entire base-excision repair pathway, as seen in heterotroph-infecting Mimiviridae These Mimiviridae encoded-enzymes were found to be monophyletic and branching at the root of the eukaryotic tree of life. This placement suggests that the last common ancestor of Mimiviridae was endowed with a large, complex genome prior to the divergence of known extant eukaryotes.IMPORTANCE Viruses on Earth are tremendously diverse in terms of morphology, functionality, and genomic composition. Over the last decade, the conceptual gap separating viruses and cellular life has tightened because of the detection of metabolic genes in viral genomes that express complex virus phenotypes upon infection. Here, we describe Prymnesium kappa virus RF01, a large alga-infecting virus with a unique morphology, an atypical infection profile, and an unprecedented number of genes involved in energy metabolism (such as the tricarboxylic (TCA) cycle and the β-oxidation pathway). Moreover, we show that the gene corresponding to one of these enzymes (the succinate dehydrogenase subunit A) is transcribed during infection and is widespread among marine viruses. This discovery provides evidence that a virus has the potential to actively regulate energy metabolism with its own gene.
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19
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RNA transfer through tunneling nanotubes. Biochem Soc Trans 2020; 49:145-160. [PMID: 33367488 DOI: 10.1042/bst20200113] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/08/2020] [Accepted: 12/10/2020] [Indexed: 02/06/2023]
Abstract
It was already suggested in the early '70's that RNA molecules might transfer between mammalian cells in culture. Yet, more direct evidence for RNA transfer in animal and plant cells was only provided decades later, as this field became established. In this mini-review, we will describe evidence for the transfer of different types of RNA between cells through tunneling nanotubes (TNTs). TNTs are long, yet thin, open-ended cellular protrusions that are structurally distinct from filopodia. TNTs connect cells and can transfer many types of cargo, including small molecules, proteins, vesicles, pathogens, and organelles. Recent work has shown that TNTs can also transfer mRNAs, viral RNAs and non-coding RNAs. Here, we will review the evidence for TNT-mediated RNA transfer, discuss the technical challenges in this field, and conjecture about the possible significance of this pathway in health and disease.
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20
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Gözen I, Dommersnes P. Biological lipid nanotubes and their potential role in evolution. THE EUROPEAN PHYSICAL JOURNAL. SPECIAL TOPICS 2020; 229:2843-2862. [PMID: 33224439 PMCID: PMC7666715 DOI: 10.1140/epjst/e2020-000130-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 08/03/2020] [Indexed: 06/11/2023]
Abstract
The membrane of cells and organelles are highly deformable fluid interfaces, and can take on a multitude of shapes. One distinctive and particularly interesting property of biological membranes is their ability to from long and uniform nanotubes. These nanoconduits are surprisingly omnipresent in all domains of life, from archaea, bacteria, to plants and mammals. Some of these tubes have been known for a century, while others were only recently discovered. Their designations are different in different branches of biology, e.g. they are called stromule in plants and tunneling nanotubes in mammals. The mechanical transformation of flat membranes to tubes involves typically a combination of membrane anchoring and external forces, leading to a pulling action that results in very rapid membrane nanotube formation - micrometer long tubes can form in a matter of seconds. Their radius is set by a mechanical balance of tension and bending forces. There also exists a large class of membrane nanotubes that form due to curvature inducing molecules. It seems plausible that nanotube formation and functionality in plants and animals may have been inherited from their bacterial ancestors during endosymbiotic evolution. Here we attempt to connect observations of nanotubes in different branches of biology, and outline their similarities and differences with the aim of providing a perspective on their joint functions and evolutionary origin.
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Affiliation(s)
- Irep Gözen
- Centre for Molecular Medicine Norway, Faculty of Medicine, University of Oslo, Oslo, 0318 Norway
- Department of Chemistry, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, 0315 Norway
- Department of Chemistry and Chemical Engineering, Chalmers University of Technology, Göteborg, 412 96 Sweden
| | - Paul Dommersnes
- Department of Physics, Norwegian University of Science and Technology, Hoegskoleringen 5, 7491 Trondheim, Norway
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21
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Chaïb A, Decossas M, Philippe C, Claisse O, Lambert O, Marrec CL. Isolation and CryoTEM of Phages Infecting Bacterial Wine Spoilers. Bio Protoc 2020; 10:e3801. [PMID: 33659455 DOI: 10.21769/bioprotoc.3801] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 08/31/2020] [Accepted: 09/22/2020] [Indexed: 11/02/2022] Open
Abstract
With the objective to isolate phages infecting wine bacterial spoilers, we designed a method for the isolation and purification of phages infecting grape-associated bacteria. The method proved successful to isolate GC1 tectivirus infecting the acetic acid bacterium Gluconobacter cerinus. The isolated phage represents a new genus within the Tectiviridae, named "Gammatectivirus". Using a traditional technique for the concentration of phage particles involving several steps of centrifugation, further insights in the ultrastructure of GC1 could be observed by cryo electron microscopy, saving time and effort. The simple workflow presented may be applied to other viruses infecting bacteria inhabiting other vegetal niches.
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Affiliation(s)
- Amel Chaïb
- University of Bordeaux, ISVV, EA4577 Œnologie, USC 1366, INRAE, Villenave d'Ornon, France
| | - Marion Decossas
- University of Bordeaux, CBMN UMR 5248, Bordeaux INP, F-33600 Pessac, France
| | - Cécile Philippe
- University of Bordeaux, ISVV, EA4577 Œnologie, USC 1366, INRAE, Villenave d'Ornon, France
| | - Olivier Claisse
- University of Bordeaux, ISVV, EA4577 Œnologie, USC 1366, INRAE, Villenave d'Ornon, France
| | - Olivier Lambert
- University of Bordeaux, CBMN UMR 5248, Bordeaux INP, F-33600 Pessac, France
| | - Claire Le Marrec
- University of Bordeaux, ISVV, EA4577 Œnologie, USC 1366, INRAE, Villenave d'Ornon, France.,ENSCBP, Bordeaux INP, F-33607 Pessac, France
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22
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Assalauova D, Kim YY, Bobkov S, Khubbutdinov R, Rose M, Alvarez R, Andreasson J, Balaur E, Contreras A, DeMirci H, Gelisio L, Hajdu J, Hunter MS, Kurta RP, Li H, McFadden M, Nazari R, Schwander P, Teslyuk A, Walter P, Xavier PL, Yoon CH, Zaare S, Ilyin VA, Kirian RA, Hogue BG, Aquila A, Vartanyants IA. An advanced workflow for single-particle imaging with the limited data at an X-ray free-electron laser. IUCRJ 2020; 7:1102-1113. [PMID: 33209321 PMCID: PMC7642788 DOI: 10.1107/s2052252520012798] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 09/21/2020] [Indexed: 05/06/2023]
Abstract
An improved analysis for single-particle imaging (SPI) experiments, using the limited data, is presented here. Results are based on a study of bacteriophage PR772 performed at the Atomic, Molecular and Optical Science instrument at the Linac Coherent Light Source as part of the SPI initiative. Existing methods were modified to cope with the shortcomings of the experimental data: inaccessibility of information from half of the detector and a small fraction of single hits. The general SPI analysis workflow was upgraded with the expectation-maximization based classification of diffraction patterns and mode decomposition on the final virus-structure determination step. The presented processing pipeline allowed us to determine the 3D structure of bacteriophage PR772 without symmetry constraints with a spatial resolution of 6.9 nm. The obtained resolution was limited by the scattering intensity during the experiment and the relatively small number of single hits.
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Affiliation(s)
- Dameli Assalauova
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Young Yong Kim
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Sergey Bobkov
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
| | - Ruslan Khubbutdinov
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation
| | - Max Rose
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Roberto Alvarez
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- School of Mathematics and Statistical Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Jakob Andreasson
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
| | - Eugeniu Balaur
- Australian Research Council Centre of Excellence in Advanced Molecular Imaging, Department of Chemistry and Physics, La Trobe Institute for Molecular Science (LIMS), La Trobe University, Melbourne, Victoria 3086, Australia
| | - Alice Contreras
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Hasan DeMirci
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Molecular Biology and Genetics, Koc University, Istanbul, 34450, Turkey
| | - Luca Gelisio
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
| | - Janos Hajdu
- Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, CZ-18221, Czech Republic
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Husargatan 3, Uppsala, SE-75124, Sweden
| | - Mark S. Hunter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | | | - Haoyuan Li
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Physics Department, Stanford University, 450 Jane Stanford Way, Stanford, CA 94305-2004, USA
| | - Matthew McFadden
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Reza Nazari
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- School for Engineering of Matter, Transport and Energy, Arizona State University, Tempe, AZ 85287, USA
| | | | - Anton Teslyuk
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation
| | - Peter Walter
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - P. Lourdu Xavier
- Center for Free Electron Laser Science (CFEL), DESY, Notkestraße 85, Hamburg, D-22607, Germany
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Max-Planck Institute for the Structure and Dynamics of Matter, Luruper Chaussee 149, Hamburg, D-22761, Germany
| | - Chun Hong Yoon
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Sahba Zaare
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Viacheslav A. Ilyin
- National Research Center ‘Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow, 123182 Russian Federation
- Moscow Institute of Physics and Technology, Moscow, 141700, Russian Federation
| | - Richard A. Kirian
- Department of Physics, Arizona State University, Tempe, Arizona AZ 85287, USA
| | - Brenda G. Hogue
- School of Life Sciences, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona AZ 85287, USA
- Biodesign Institute, Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287, USA
| | - Andrew Aquila
- SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestraße 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe sh. 31, Moscow, 115409, Russian Federation
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23
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Quemin ERJ, Machala EA, Vollmer B, Pražák V, Vasishtan D, Rosch R, Grange M, Franken LE, Baker LA, Grünewald K. Cellular Electron Cryo-Tomography to Study Virus-Host Interactions. Annu Rev Virol 2020; 7:239-262. [PMID: 32631159 DOI: 10.1146/annurev-virology-021920-115935] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Viruses are obligatory intracellular parasites that reprogram host cells upon infection to produce viral progeny. Here, we review recent structural insights into virus-host interactions in bacteria, archaea, and eukaryotes unveiled by cellular electron cryo-tomography (cryoET). This advanced three-dimensional imaging technique of vitreous samples in near-native state has matured over the past two decades and proven powerful in revealing molecular mechanisms underlying viral replication. Initial studies were restricted to cell peripheries and typically focused on early infection steps, analyzing surface proteins and viral entry. Recent developments including cryo-thinning techniques, phase-plate imaging, and correlative approaches have been instrumental in also targeting rare events inside infected cells. When combined with advances in dedicated image analyses and processing methods, details of virus assembly and egress at (sub)nanometer resolution were uncovered. Altogether, we provide a historical and technical perspective and discuss future directions and impacts of cryoET for integrative structural cell biology analyses of viruses.
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Affiliation(s)
- Emmanuelle R J Quemin
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Emily A Machala
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Benjamin Vollmer
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Vojtěch Pražák
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Daven Vasishtan
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Rene Rosch
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Michael Grange
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Linda E Franken
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
| | - Lindsay A Baker
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
| | - Kay Grünewald
- Centre for Structural Systems Biology, Heinrich-Pette-Institute, Leibniz Institute for Experimental Virology, University of Hamburg, D-22607 Hamburg, Germany;
- Division of Structural Biology, Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, United Kingdom
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24
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Dion MB, Oechslin F, Moineau S. Phage diversity, genomics and phylogeny. Nat Rev Microbiol 2020; 18:125-138. [PMID: 32015529 DOI: 10.1038/s41579-019-0311-5] [Citation(s) in RCA: 492] [Impact Index Per Article: 98.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/05/2019] [Indexed: 12/23/2022]
Abstract
Recent advances in viral metagenomics have enabled the rapid discovery of an unprecedented catalogue of phages in numerous environments, from the human gut to the deep ocean. Although these advances have expanded our understanding of phage genomic diversity, they also revealed that we have only scratched the surface in the discovery of novel viruses. Yet, despite the remarkable diversity of phages at the nucleotide sequence level, the structural proteins that form viral particles show strong similarities and conservation. Phages are uniquely interconnected from an evolutionary perspective and undergo multiple events of genetic exchange in response to the selective pressure of their hosts, which drives their diversity. In this Review, we explore phage diversity at the structural, genomic and community levels as well as the complex evolutionary relationships between phages, moulded by the mosaicity of their genomes.
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Affiliation(s)
- Moïra B Dion
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Frank Oechslin
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada.,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada
| | - Sylvain Moineau
- Département de biochimie, de microbiologie et de bio-informatique, Faculté des sciences et de génie, Université Laval, Québec City, Québec, Canada. .,Groupe de recherche en écologie buccale, Faculté de médecine dentaire, Université Laval, Québec City, Québec, Canada. .,Félix d'Hérelle Reference Center for Bacterial Viruses, Université Laval, Québec City, Québec, Canada.
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25
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A Novel Genus of Actinobacterial Tectiviridae. Viruses 2019; 11:v11121134. [PMID: 31817897 PMCID: PMC6950372 DOI: 10.3390/v11121134] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Revised: 12/03/2019] [Accepted: 12/04/2019] [Indexed: 01/31/2023] Open
Abstract
Streptomyces phages WheeHeim and Forthebois are two novel members of the Tectiviridae family. These phages were isolated on cultures of the plant pathogen Streptomyces scabiei, known for its worldwide economic impact on potato crops. Transmission electron microscopy showed viral particles with double-layered icosahedral capsids, and frequent instances of protruding nanotubes harboring a collar-like structure. Mass-spectrometry confirmed the presence of lipids in the virion, and serial purification of colonies from turbid plaques and immunity testing revealed that both phages are temperate. Streptomycesphages WheeHeim and Forthebois have linear dsDNA chromosomes (18,266 bp and 18,251 bp long, respectively) with the characteristic two-segment architecture of the Tectiviridae. Both genomes encode homologs of the canonical tectiviral proteins (major capsid protein, packaging ATPase and DNA polymerase), as well as PRD1-type virion-associated transglycosylase and membrane DNA delivery proteins. Comparative genomics and phylogenetic analyses firmly establish that these two phages, together with Rhodococcusphage Toil, form a new genus within the Tectiviridae, which we have tentatively named Deltatectivirus. The identification of a cohesive clade of Actinobacteria-infecting tectiviruses with conserved genome structure but with scant sequence similarity to members of other tectiviral genera confirms that the Tectiviridae are an ancient lineage infecting a broad range of bacterial hosts.
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26
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Hartman R, Eilers BJ, Bollschweiler D, Munson-McGee JH, Engelhardt H, Young MJ, Lawrence CM. The Molecular Mechanism of Cellular Attachment for an Archaeal Virus. Structure 2019; 27:1634-1646.e3. [PMID: 31587916 DOI: 10.1016/j.str.2019.09.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 08/21/2019] [Accepted: 09/16/2019] [Indexed: 12/17/2022]
Abstract
Sulfolobus turreted icosahedral virus (STIV) is a model archaeal virus and member of the PRD1-adenovirus lineage. Although STIV employs pyramidal lysis structures to exit the host, knowledge of the viral entry process is lacking. We therefore initiated studies on STIV attachment and entry. Negative stain and cryoelectron micrographs showed virion attachment to pili-like structures emanating from the Sulfolobus host. Tomographic reconstruction and sub-tomogram averaging revealed pili recognition by the STIV C381 turret protein. Specifically, the triple jelly roll structure of C381 determined by X-ray crystallography shows that pilus recognition is mediated by conserved surface residues in the second and third domains. In addition, the STIV petal protein (C557), when present, occludes the pili binding site, suggesting that it functions as a maturation protein. Combined, these results demonstrate a role for the namesake STIV turrets in initial cellular attachment and provide the first molecular model for viral attachment in the archaeal domain of life.
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Affiliation(s)
- Ross Hartman
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Brian J Eilers
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA
| | - Daniel Bollschweiler
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | - Jacob H Munson-McGee
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA
| | - Harald Engelhardt
- Department of Molecular Structural Biology, Max-Planck-Institute for Biochemistry, Martinsried, Germany
| | - Mark J Young
- Department of Microbiology and Immunology, Montana State University, Bozeman, MT 59717, USA; Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA; The Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
| | - C Martin Lawrence
- Department of Chemistry and Biochemistry, Montana State University, Bozeman, MT 59717, USA; The Thermal Biology Institute, Montana State University, Bozeman, MT 59717, USA.
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27
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Reddy HK, Carroni M, Hajdu J, Svenda M. Electron cryo-microscopy of bacteriophage PR772 reveals the elusive vertex complex and the capsid architecture. eLife 2019; 8:48496. [PMID: 31513011 PMCID: PMC6750898 DOI: 10.7554/elife.48496] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 09/09/2019] [Indexed: 12/22/2022] Open
Abstract
Bacteriophage PR772, a member of the Tectiviridae family, has a 70 nm diameter icosahedral protein capsid that encapsulates a lipid membrane, dsDNA, and various internal proteins. An icosahedrally averaged CryoEM reconstruction of the wild-type virion and a localized reconstruction of the vertex region reveal the composition and the structure of the vertex complex along with new protein conformations that play a vital role in maintaining the capsid architecture of the virion. The overall resolution of the virion is 2.75 Å, while the resolution of the protein capsid is 2.3 Å. The conventional penta-symmetron formed by the capsomeres is replaced by a large vertex complex in the pseudo T = 25 capsid. All the vertices contain the host-recognition protein, P5; two of these vertices show the presence of the receptor-binding protein, P2. The 3D structure of the vertex complex shows interactions with the viral membrane, indicating a possible mechanism for viral infection.
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Affiliation(s)
- Hemanth Kn Reddy
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden
| | - Marta Carroni
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Janos Hajdu
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden.,Institute of Physics, ELI Beamlines, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Martin Svenda
- Department of Cell and Molecular Biology, Laboratory of Molecular Biophysics, Uppsala University, Uppsala, Sweden.,Department of Applied Physics, Biomedical and X-Ray Physics, KTH Royal Institute of Technology, Stockholm, Sweden
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28
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Survey of high-resolution archaeal virus structures. Curr Opin Virol 2019; 36:74-83. [PMID: 31238245 DOI: 10.1016/j.coviro.2019.05.008] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Revised: 04/30/2019] [Accepted: 05/09/2019] [Indexed: 01/21/2023]
Abstract
Archaeal viruses exhibit diverse morphologies whose structures are just beginning to be explored at high-resolution. In this review, we update recent findings on archaeal structural proteins and virion architectures and place them in the biological context in which these viruses replicate. We conclude that many of the unusual structural features and dynamics of archaeal viruses aid their replication and survival in the chemically harsh environments, in which they replicate. Furthermore, we should expect to find more novel features from examining the high-resolution structures of additional archaeal viruses.
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Abstract
Cryo-electron tomography (cryo-ET) allows three-dimensional (3D) visualization of frozen-hydrated biological samples, such as protein complexes and cell organelles, in near-native environments at nanometer scale. Protein complexes that are present in multiple copies in a set of tomograms can be extracted, mutually aligned, and averaged to yield a signal-enhanced 3D structure up to sub-nanometer or even near-atomic resolution. This technique, called subtomogram averaging (StA), is powered by improvements in EM hardware and image processing software. Importantly, StA provides unique biological insights into the structure and function of cellular machinery in close-to-native contexts. In this chapter, we describe the principles and key steps of StA. We briefly cover sample preparation and data collection with an emphasis on image processing procedures related to tomographic reconstruction, subtomogram alignment, averaging, and classification. We conclude by summarizing current limitations and future directions of this technique with a focus on high-resolution StA.
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30
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Pergu R, Dagar S, Kumar H, Kumar R, Bhattacharya J, Mylavarapu SVS. The chaperone ERp29 is required for tunneling nanotube formation by stabilizing MSec. J Biol Chem 2019; 294:7177-7193. [PMID: 30877198 DOI: 10.1074/jbc.ra118.005659] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 02/14/2019] [Indexed: 01/23/2023] Open
Abstract
Tunneling nanotubes (TNTs) are membrane conduits that mediate long-distance intercellular cross-talk in several organisms and play vital roles during development, pathogenic transmission, and cancer metastasis. However, the molecular mechanisms of TNT formation and function remain poorly understood. The protein MSec (also known as TNFα-induced protein 2 (TNFAIP2) and B94) is essential for TNT formation in multiple cell types. Here, using affinity protein purification, mass spectrometric identification, and confocal immunofluorescence microscopy assays, we found that MSec interacts with the endoplasmic reticulum (ER) chaperone ERp29. siRNA-mediated ERp29 depletion in mammalian cells significantly reduces TNT formation, whereas its overexpression induces TNT formation, but in a strictly MSec-dependent manner. ERp29 stabilized MSec protein levels, but not its mRNA levels, and the chaperone activity of ERp29 was required for maintaining MSec protein stability. Subcellular ER fractionation and subsequent limited proteolytic treatment suggested that MSec is associated with the outer surface of the ER. The ERp29-MSec interaction appeared to require the presence of other bridging protein(s), perhaps triggered by post-translational modification of ERp29. Our study implicates MSec as a target of ERp29 and reveals an indispensable role for the ER in TNT formation, suggesting new modalities for regulating TNT numbers in cells and tissues.
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Affiliation(s)
- Rajaiah Pergu
- From the Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, and.,the Manipal Academy of Higher Education, Manipal Karnataka 576104, and
| | - Sunayana Dagar
- From the Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, and.,the Kalinga Institute of Industrial Technology, Bhubaneswar Odisha 751024, India
| | - Harsh Kumar
- From the Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, and.,the Manipal Academy of Higher Education, Manipal Karnataka 576104, and
| | - Rajesh Kumar
- the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad Haryana 121001
| | - Jayanta Bhattacharya
- the HIV Vaccine Translational Research Laboratory, Translational Health Science and Technology Institute, NCR Biotech Science Cluster, Faridabad Haryana 121001
| | - Sivaram V S Mylavarapu
- From the Laboratory of Cellular Dynamics, Regional Centre for Biotechnology, and .,the Manipal Academy of Higher Education, Manipal Karnataka 576104, and.,the Kalinga Institute of Industrial Technology, Bhubaneswar Odisha 751024, India
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31
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Shi Y, Yin K, Tai X, DeMirci H, Hosseinizadeh A, Hogue BG, Li H, Ourmazd A, Schwander P, Vartanyants IA, Yoon CH, Aquila A, Liu H. Evaluation of the performance of classification algorithms for XFEL single-particle imaging data. IUCRJ 2019; 6:331-340. [PMID: 30867930 PMCID: PMC6400180 DOI: 10.1107/s2052252519001854] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/31/2019] [Indexed: 05/22/2023]
Abstract
Using X-ray free-electron lasers (XFELs), it is possible to determine three-dimensional structures of nanoscale particles using single-particle imaging methods. Classification algorithms are needed to sort out the single-particle diffraction patterns from the large amount of XFEL experimental data. However, different methods often yield inconsistent results. This study compared the performance of three classification algorithms: convolutional neural network, graph cut and diffusion map manifold embedding methods. The identified single-particle diffraction data of the PR772 virus particles were assembled in the three-dimensional Fourier space for real-space model reconstruction. The comparison showed that these three classification methods lead to different datasets and subsequently result in different electron density maps of the reconstructed models. Interestingly, the common dataset selected by these three methods improved the quality of the merged diffraction volume, as well as the resolutions of the reconstructed maps.
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Affiliation(s)
- Yingchen Shi
- Department of Engineering Physics, Tsinghua University, 30 Shuangqing Rd, Haidian, Beijing 100084, People’s Republic of China
- Complex Systems Division, Beijing Computational Science Research Centre, 8 E Xibeiwang Rd, Haidian, Beijing 100193, People’s Republic of China
| | - Ke Yin
- Center for Mathematical Sciences, Huazhong University of Science and Technology, Wuhan, Hubei 430074, People’s Republic of China
| | - Xuecheng Tai
- Department of Mathematics, University of Bergen, PO Box 7800, Bergen, 5020, Norway
| | - Hasan DeMirci
- Biosciences Division, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin USA
| | - Brenda G. Hogue
- Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute at Arizona State University, Tempe, 85287, USA
| | - Haoyuan Li
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
- Department of Physics, Stanford University, 450 Serra Mall, Stanford, CA 94305, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin–Milwaukee, Milwaukee, Wisconsin USA
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg, D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, Moscow, 115409, Russian Federation
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Haiguang Liu
- Complex Systems Division, Beijing Computational Science Research Centre, 8 E Xibeiwang Rd, Haidian, Beijing 100193, People’s Republic of China
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32
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Mäntynen S, Sundberg LR, Oksanen HM, Poranen MM. Half a Century of Research on Membrane-Containing Bacteriophages: Bringing New Concepts to Modern Virology. Viruses 2019; 11:E76. [PMID: 30669250 PMCID: PMC6356626 DOI: 10.3390/v11010076] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Revised: 01/15/2019] [Accepted: 01/16/2019] [Indexed: 12/14/2022] Open
Abstract
Half a century of research on membrane-containing phages has had a major impact on virology, providing new insights into virus diversity, evolution and ecological importance. The recent revolutionary technical advances in imaging, sequencing and lipid analysis have significantly boosted the depth and volume of knowledge on these viruses. This has resulted in new concepts of virus assembly, understanding of virion stability and dynamics, and the description of novel processes for viral genome packaging and membrane-driven genome delivery to the host. The detailed analyses of such processes have given novel insights into DNA transport across the protein-rich lipid bilayer and the transformation of spherical membrane structures into tubular nanotubes, resulting in the description of unexpectedly dynamic functions of the membrane structures. Membrane-containing phages have provided a framework for understanding virus evolution. The original observation on membrane-containing bacteriophage PRD1 and human pathogenic adenovirus has been fundamental in delineating the concept of "viral lineages", postulating that the fold of the major capsid protein can be used as an evolutionary fingerprint to trace long-distance evolutionary relationships that are unrecognizable from the primary sequences. This has brought the early evolutionary paths of certain eukaryotic, bacterial, and archaeal viruses together, and potentially enables the reorganization of the nearly immeasurable virus population (~1 × 1031) on Earth into a reasonably low number of groups representing different architectural principles. In addition, the research on membrane-containing phages can support the development of novel tools and strategies for human therapy and crop protection.
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Affiliation(s)
- Sari Mäntynen
- Center of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
- Department of Microbiology and Molecular Genetics, University of California, Davis, CA 95616, USA.
| | - Lotta-Riina Sundberg
- Center of Excellence in Biological Interactions, Department of Biological and Environmental Science and Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland.
| | - Hanna M Oksanen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
| | - Minna M Poranen
- Molecular and Integrative Biosciences Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, FI-00014 Helsinki, Finland.
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33
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Membrane-Containing Icosahedral Bacteriophage PRD1: The Dawn of Viral Lineages. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:85-109. [DOI: 10.1007/978-3-030-14741-9_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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34
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San Martín C. Virus Maturation. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2019; 1215:129-158. [DOI: 10.1007/978-3-030-14741-9_7] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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35
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Rose M, Bobkov S, Ayyer K, Kurta RP, Dzhigaev D, Kim YY, Morgan AJ, Yoon CH, Westphal D, Bielecki J, Sellberg JA, Williams G, Maia FR, Yefanov OM, Ilyin V, Mancuso AP, Chapman HN, Hogue BG, Aquila A, Barty A, Vartanyants IA. Single-particle imaging without symmetry constraints at an X-ray free-electron laser. IUCRJ 2018; 5:727-736. [PMID: 30443357 PMCID: PMC6211532 DOI: 10.1107/s205225251801120x] [Citation(s) in RCA: 51] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 08/06/2018] [Indexed: 05/19/2023]
Abstract
The analysis of a single-particle imaging (SPI) experiment performed at the AMO beamline at LCLS as part of the SPI initiative is presented here. A workflow for the three-dimensional virus reconstruction of the PR772 bacteriophage from measured single-particle data is developed. It consists of several well defined steps including single-hit diffraction data classification, refined filtering of the classified data, reconstruction of three-dimensional scattered intensity from the experimental diffraction patterns by orientation determination and a final three-dimensional reconstruction of the virus electron density without symmetry constraints. The analysis developed here revealed and quantified nanoscale features of the PR772 virus measured in this experiment, with the obtained resolution better than 10 nm, with a clear indication that the structure was compressed in one direction and, as such, deviates from ideal icosahedral symmetry.
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Affiliation(s)
- Max Rose
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg D-22607, Germany
| | - Sergey Bobkov
- National Research Centre ’Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow 123182, Russia
| | - Kartik Ayyer
- Center for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, Germany
| | | | - Dmitry Dzhigaev
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg D-22607, Germany
| | - Young Yong Kim
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg D-22607, Germany
| | - Andrew J. Morgan
- Center for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, Germany
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Daniel Westphal
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Johan Bielecki
- European XFEL GmbH, Holzkoppel 4, Schenefeld 22869, Germany
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Sweden
| | - Jonas A. Sellberg
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Sweden
- Biomedical and X-Ray Physics, Department of Applied Physics, AlbaNova University Center, KTH Royal Institute of Technology, Stockholm SE-106 91, Sweden
| | - Garth Williams
- Brookhaven National Laboratory, 98 Rochester St, Shirley, NY 11967, USA
| | - Filipe R.N.C. Maia
- Laboratory of Molecular Biophysics, Department of Cell and Molecular Biology, Uppsala University, Sweden
- NERSC, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Olexander M. Yefanov
- Center for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, Germany
| | - Vyacheslav Ilyin
- National Research Centre ’Kurchatov Institute’, Akademika Kurchatova pl. 1, Moscow 123182, Russia
| | | | - Henry N. Chapman
- Center for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, Germany
| | - Brenda G. Hogue
- Biodesign Center for Immunotherapy, Vaccines, and Virotherapy, Biodesign Institute at Arizona State University, Tempe 85287, USA
- Biodesign Center for Applied Structural Discovery, Biodesign Institute at Arizona State University, Tempe, AZ 85287, USA
- Arizona State University, School of Life Sciences (SOLS), Tempe, AZ 85287, USA
| | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, 2575 Sand Hill Road, Menlo Park, CA 94025, USA
| | - Anton Barty
- Center for Free Electron Laser Science (CFEL), Notkestrasse 85, Hamburg 22607, Germany
| | - Ivan A. Vartanyants
- Deutsches Elektronen-Synchrotron DESY, Notkestrasse 85, Hamburg D-22607, Germany
- National Research Nuclear University MEPhI (Moscow Engineering Physics Institute), Kashirskoe shosse 31, Moscow 115409, Russia
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36
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Sasidharan S, Bradford SA, Šimůnek J, Torkzaban S. Minimizing Virus Transport in Porous Media by Optimizing Solid Phase Inactivation. JOURNAL OF ENVIRONMENTAL QUALITY 2018; 47:1058-1067. [PMID: 30272798 DOI: 10.2134/jeq2018.01.0027] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The influence of virus type (PRD1 and ΦX174), temperature (flow at 4 and 20°C), a no-flow storage duration (0, 36, 46, and 70 d), and temperature cycling (flow at 20°C and storage at 4°C) on virus transport and fate were investigated in saturated sand-packed columns. The vast majority (84-99.5%) of viruses were irreversibly retained on the sand, even in the presence of deionized water and beef extract at pH = 11. The reversibly retained virus fraction () was small (1.6 × 10 to 0.047) but poses a risk of long-term virus contamination. The value of and associated transport risk was lower at a higher temperature and for increases in the no-flow storage period due to the temperature dependency of the solid phase inactivation. A model that considered advective-dispersive transport, attachment (), detachment (), solid phase inactivation (μ), and liquid phase inactivation (μ) coefficients, and a Langmuirian blocking function provided a good description of the early portion of the breakthrough curve. The removal parameters were found to be in the order of > μ >> μ. Furthermore, μ was an order of magnitude higher than μ for PRD1, whereas μ was two and three orders of magnitude higher than μ for ΦX174 at 4 and 20°C, respectively. Transport modeling with two retention, release, and inactivation sites demonstrated that a small fraction of viruses exhibited a much slower release and solid phase inactivation rate, presumably because variations in the sand and virus surface roughness caused differences in the strength of adhesion. These findings demonstrate the importance of solid phase inactivation, temperature, and storage periods in eliminating virus transport in porous media. This research has potential implications for managed aquifer recharge applications and guidelines to enhance the virus removal by controlling the temperature and aquifer residence time.
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37
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Yamashita YM, Inaba M, Buszczak M. Specialized Intercellular Communications via Cytonemes and Nanotubes. Annu Rev Cell Dev Biol 2018; 34:59-84. [PMID: 30074816 DOI: 10.1146/annurev-cellbio-100617-062932] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
In recent years, thin membrane protrusions such as cytonemes and tunneling nanotubes have emerged as a novel mechanism of intercellular communication. Protrusion-based cellular interactions allow for specific communication between participating cells and have a distinct spectrum of advantages compared to secretion- and diffusion-based intercellular communication. Identification of protrusion-based signaling in diverse systems suggests that this mechanism is a ubiquitous and prevailing means of communication employed by many cell types. Moreover, accumulating evidence indicates that protrusion-based intercellular communication is often involved in pathogenesis, including cancers and infections. Here we review our current understanding of protrusion-based intercellular communication.
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Affiliation(s)
- Yukiko M Yamashita
- Life Sciences Institute, Department of Cell and Developmental Biology, and Howard Hughes Medical Institute, University of Michigan, Ann Arbor, Michigan 48109, USA;
| | - Mayu Inaba
- Department of Cell Biology, University of Connecticut Health Center, Farmington, Connecticut 06030, USA;
| | - Michael Buszczak
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, Texas 75390, USA;
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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: 1.4] [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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Azinas S, Bano F, Torca I, Bamford DH, Schwartz GA, Esnaola J, Oksanen HM, Richter RP, Abrescia NG. Membrane-containing virus particles exhibit the mechanics of a composite material for genome protection. NANOSCALE 2018; 10:7769-7779. [PMID: 29658555 PMCID: PMC5944389 DOI: 10.1039/c8nr00196k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 03/02/2018] [Indexed: 06/08/2023]
Abstract
The protection of the viral genome during extracellular transport is an absolute requirement for virus survival and replication. In addition to the almost universal proteinaceous capsids, certain viruses add a membrane layer that encloses their double-stranded (ds) DNA genome within the protein shell. Using the membrane-containing enterobacterial virus PRD1 as a prototype, and a combination of nanoindentation assays by atomic force microscopy and finite element modelling, we show that PRD1 provides a greater stability against mechanical stress than that achieved by the majority of dsDNA icosahedral viruses that lack a membrane. We propose that the combination of a stiff and brittle proteinaceous shell coupled with a soft and compliant membrane vesicle yields a tough composite nanomaterial well-suited to protect the viral DNA during extracellular transport.
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Affiliation(s)
- S. Azinas
- Molecular recognition and host–pathogen interactions programme , CIC bioGUNE , CIBERehd , Derio , Spain
- Biosurfaces Lab , CIC biomaGUNE , San Sebastian , Spain
| | - F. Bano
- Biosurfaces Lab , CIC biomaGUNE , San Sebastian , Spain
| | - I. Torca
- Mechanical and Industrial Production Department , Mondragon University , Arrasate-Mondragón , Spain
| | - D. H. Bamford
- Molecular and Integrative Biosciences Research Programme , Faculty of Biological and Environmental Sciences , Viikki Biocenter , University of Helsinki , Finland
| | - G. A. Schwartz
- Centro de Física de Materiales , (CSIC-UPV/EHU) & Donostia International Physics Center , San Sebastian , Spain
| | - J. Esnaola
- Mechanical and Industrial Production Department , Mondragon University , Arrasate-Mondragón , Spain
| | - H. M. Oksanen
- Molecular and Integrative Biosciences Research Programme , Faculty of Biological and Environmental Sciences , Viikki Biocenter , University of Helsinki , Finland
| | - R. P. Richter
- Biosurfaces Lab , CIC biomaGUNE , San Sebastian , Spain
- School of Biomedical Sciences , Faculty of Biological Sciences , School of Physics and Astronomy , Faculty of Mathematics and Physical Sciences , and Astbury Centre for Structural Molecular Biology University of Leeds , Leeds , UK . ; Tel: +44 113 3431969
| | - N. G. Abrescia
- Molecular recognition and host–pathogen interactions programme , CIC bioGUNE , CIBERehd , Derio , Spain
- IKERBASQUE , Basque Foundation for Science , Bilbao , Spain . ; Fax: +34 946572502 ; Tel: +34 946572523
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40
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Breaking Symmetry in Viral Icosahedral Capsids as Seen through the Lenses of X-ray Crystallography and Cryo-Electron Microscopy. Viruses 2018; 10:v10020067. [PMID: 29414851 PMCID: PMC5850374 DOI: 10.3390/v10020067] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2018] [Revised: 01/26/2018] [Accepted: 01/31/2018] [Indexed: 12/19/2022] Open
Abstract
The majority of viruses on Earth form capsids built by multiple copies of one or more types of a coat protein arranged with 532 symmetry, generating an icosahedral shell. This highly repetitive structure is ideal to closely pack identical protein subunits and to enclose the nucleic acid genomes. However, the icosahedral capsid is not merely a passive cage but undergoes dynamic events to promote packaging, maturation and the transfer of the viral genome into the host. These essential processes are often mediated by proteinaceous complexes that interrupt the shell’s icosahedral symmetry, providing a gateway through the capsid. In this review, we take an inventory of molecular structures observed either internally, or at the 5-fold vertices of icosahedral DNA viruses that infect bacteria, archea and eukaryotes. Taking advantage of the recent revolution in cryo-electron microscopy (cryo-EM) and building upon a wealth of crystallographic structures of individual components, we review the design principles of non-icosahedral structural components that interrupt icosahedral symmetry and discuss how these macromolecules play vital roles in genome packaging, ejection and host receptor-binding.
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Kauffman KM, Hussain FA, Yang J, Arevalo P, Brown JM, Chang WK, VanInsberghe D, Elsherbini J, Sharma RS, Cutler MB, Kelly L, Polz MF. A major lineage of non-tailed dsDNA viruses as unrecognized killers of marine bacteria. Nature 2018; 554:118-122. [DOI: 10.1038/nature25474] [Citation(s) in RCA: 123] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2016] [Accepted: 12/28/2017] [Indexed: 02/06/2023]
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Philippe C, Krupovic M, Jaomanjaka F, Claisse O, Petrel M, le Marrec C. Bacteriophage GC1, a Novel Tectivirus Infecting Gluconobacter Cerinus, an Acetic Acid Bacterium Associated with Wine-Making. Viruses 2018; 10:v10010039. [PMID: 29337868 PMCID: PMC5795452 DOI: 10.3390/v10010039] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2017] [Revised: 01/05/2018] [Accepted: 01/12/2018] [Indexed: 12/22/2022] Open
Abstract
The Gluconobacter phage GC1 is a novel member of the Tectiviridae family isolated from a juice sample collected during dry white wine making. The bacteriophage infects Gluconobacter cerinus, an acetic acid bacterium which represents a spoilage microorganism during wine making, mainly because it is able to produce ethyl alcohol and transform it into acetic acid. Transmission electron microscopy revealed tail-less icosahedral particles with a diameter of ~78 nm. The linear double-stranded DNA genome of GC1 (16,523 base pairs) contains terminal inverted repeats and carries 36 open reading frames, only a handful of which could be functionally annotated. These encode for the key proteins involved in DNA replication (protein-primed family B DNA polymerase) as well as in virion structure and assembly (major capsid protein, genome packaging ATPase (adenosine triphosphatase) and several minor capsid proteins). GC1 is the first tectivirus infecting an alphaproteobacterial host and is thus far the only temperate tectivirus of gram-negative bacteria. Based on distinctive sequence and life-style features, we propose that GC1 represents a new genus within the Tectiviridae, which we tentatively named “Gammatectivirus”. Furthermore, GC1 helps to bridge the gap in the sequence space between alphatectiviruses and betatectiviruses.
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Affiliation(s)
- Cécile Philippe
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
| | - Mart Krupovic
- Department of Microbiology, Institut Pasteur, 75015 Paris, France.
| | - Fety Jaomanjaka
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
| | - Olivier Claisse
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
- Institut National de la Recherche Agronomique (INRA), ISVV, Unité Sous Contrat 1366 Oenologie, 33882 Villenave d'Ornon, France.
| | - Melina Petrel
- Bordeaux Imaging Center, University Bordeaux, Unité Mixte de Service 3420 CNRS-Unité de Service 4, Institut National de la Santé et de la Recherche Médicale, 33076 Bordeaux, France.
| | - Claire le Marrec
- Institut des Sciences de la Vigne et du Vin (ISVV), University Bordeaux, Equipe d'Accueil 4577, Unité de Recherche Oenologie, 33882 Villenave d'Ornon, France.
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43
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Furfaro LL, Chang BJ, Payne MS. Applications for Bacteriophage Therapy during Pregnancy and the Perinatal Period. Front Microbiol 2018; 8:2660. [PMID: 29375525 PMCID: PMC5768649 DOI: 10.3389/fmicb.2017.02660] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Accepted: 12/20/2017] [Indexed: 12/19/2022] Open
Abstract
Pregnant women and their unborn children are a population that is particularly vulnerable to bacterial infection. Physiological changes that occur during pregnancy affect the way women respond to such infections and the options that clinicians have for treatment. Antibiotics are still considered the best option for active infections and a suitable prophylaxis for prevention of potential infections, such as vaginal/rectal Streptococcus agalactiae colonization prior to birth. The effect of such antibiotic use on the developing fetus, however, is still largely unknown. Recent research has suggested that the fetal gut microbiota plays a critical role in fetal immunologic programming. Hence, even minor alterations in this microbiota may have potentially significant downstream effects. An ideal antibacterial therapeutic for administration during pregnancy would be one that is highly specific for its target, leaving the surrounding microbiota intact. This review first provides a basic overview of the challenges a clinician faces when administering therapeutics to a pregnant patient and then goes on to explore common bacterial infections in pregnancy, use of antibiotics for treatment/prevention of such infections and the consequences of such treatment for the mother and infant. With this background established, the review then explores the potential for use of bacteriophage (phage) therapy as an alternative to antibiotics during the antenatal period. Many previous reviews have highlighted the revitalization of and potential for phage therapy for treatment of a range of bacterial infections, particularly in the context of the increasing threat of widespread antibiotic resistance. However, information on the potential for the use of phage therapeutics in pregnancy is lacking. This review aims to provide a thorough overview of studies of this nature and discuss the feasibility of bacteriophage use during pregnancy to treat and/or prevent bacterial infections.
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Affiliation(s)
- Lucy L. Furfaro
- Division of Obstetrics and Gynecology, School of Medicine, The University of Western Australia, Crawley, WA, Australia
| | - Barbara J. Chang
- Marshall Centre for Infectious Disease Research and Training, School of Biomedical Sciences, The University of Western Australia, Crawley, WA, Australia
| | - Matthew S. Payne
- Division of Obstetrics and Gynecology, School of Medicine, The University of Western Australia, Crawley, WA, Australia
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Sáenz-de-Santa-María I, Bernardo-Castiñeira C, Enciso E, García-Moreno I, Chiara JL, Suarez C, Chiara MD. Control of long-distance cell-to-cell communication and autophagosome transfer in squamous cell carcinoma via tunneling nanotubes. Oncotarget 2017; 8:20939-20960. [PMID: 28423494 PMCID: PMC5400557 DOI: 10.18632/oncotarget.15467] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Accepted: 02/06/2017] [Indexed: 12/20/2022] Open
Abstract
Tunneling nanotubes (TnTs) are thin channels that temporally connect nearby cells allowing the cell-to-cell trafficking of biomolecules and organelles. The presence or absence of TnTs in human neoplasms and the mechanisms of TnT assembly remains largely unexplored. In this study, we have identified TnTs in tumor cells derived from squamous cell carcinomas (SCC) cultured under bi-dimensional and tri-dimensional conditions and also in human SCC tissues. Our study demonstrates that TnTs are not specific of epithelial or mesenchymal phenotypes and allow the trafficking of endosomal/lysosomal vesicles, mitochondria, and autophagosomes between both types of cells. We have identified focal adhesion kinase (FAK) as a key molecule required for TnT assembly via a mechanism involving the MMP-2 metalloprotease. We have also found that the FAK inhibitor PF-562271, which is currently in clinical development for cancer treatment, impairs TnT formation. Finally, FAK-deficient cells transfer lysosomes/autophagosomes to FAK-proficient cells via TnTs which may represent a novel mechanism to adapt to the stress elicited by impaired FAK signaling. Collectively, our results strongly suggest a link between FAK, MMP-2, and TnT, and unveil new vulnerabilities that can be exploited to efficiently eradicate cancer cells.
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Affiliation(s)
- Inés Sáenz-de-Santa-María
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias, Instituto Universitario de Oncología del Principado de Asturias, CIBERONC, Universidad de Oviedo, Oviedo, Spain
| | - Cristóbal Bernardo-Castiñeira
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias, Instituto Universitario de Oncología del Principado de Asturias, CIBERONC, Universidad de Oviedo, Oviedo, Spain
| | - Eduardo Enciso
- Facultad de Ciencias Químicas, Universidad Complutense de Madrid, Madrid, Spain
| | | | | | - Carlos Suarez
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias, Instituto Universitario de Oncología del Principado de Asturias, CIBERONC, Universidad de Oviedo, Oviedo, Spain
| | - María-Dolores Chiara
- Servicio de Otorrinolaringología, Hospital Universitario Central de Asturias, Instituto Universitario de Oncología del Principado de Asturias, CIBERONC, Universidad de Oviedo, Oviedo, Spain
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45
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Milrot E, Shimoni E, Dadosh T, Rechav K, Unger T, Van Etten JL, Minsky A. Structural studies demonstrating a bacteriophage-like replication cycle of the eukaryote-infecting Paramecium bursaria chlorella virus-1. PLoS Pathog 2017; 13:e1006562. [PMID: 28850602 PMCID: PMC5593192 DOI: 10.1371/journal.ppat.1006562] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Revised: 09/11/2017] [Accepted: 07/31/2017] [Indexed: 11/18/2022] Open
Abstract
A fundamental stage in viral infection is the internalization of viral genomes in host cells. Although extensively studied, the mechanisms and factors responsible for the genome internalization process remain poorly understood. Here we report our observations, derived from diverse imaging methods on genome internalization of the large dsDNA Paramecium bursaria chlorella virus-1 (PBCV-1). Our studies reveal that early infection stages of this eukaryotic-infecting virus occurs by a bacteriophage-like pathway, whereby PBCV-1 generates a hole in the host cell wall and ejects its dsDNA genome in a linear, base-pair-by-base-pair process, through a membrane tunnel generated by the fusion of the virus internal membrane with the host membrane. Furthermore, our results imply that PBCV-1 DNA condensation that occurs shortly after infection probably plays a role in genome internalization, as hypothesized for the infection of some bacteriophages. The subsequent perforation of the host photosynthetic membranes presumably enables trafficking of viral genomes towards host nuclei. Previous studies established that at late infection stages PBCV-1 generates cytoplasmic organelles, termed viral factories, where viral assembly takes place, a feature characteristic of many large dsDNA viruses that infect eukaryotic organisms. PBCV-1 thus appears to combine a bacteriophage-like mechanism during early infection stages with a eukaryotic-like infection pathway in its late replication cycle. Although extensively studied, the mechanisms responsible for internalization of viral genomes into their host cells remain unclear. A particularly interesting case of genome release and internalization is provided by the large Paramecium bursaria chlorella virus-1 (PBCV-1), which infects unicellular eukaryotic photosynthetic chlorella cells. In order to release its long dsDNA genome and to enable its translocation to the host nucleus, PBCV-1 must overcome multiple hurdles, including a thick host cell wall and multilayered chloroplast membranes that surround the host cytoplasm. Our observations indicate that these obstacles are dealt with perforations of the host wall, the host cellular membrane, and the host photosynthetic membranes by viral-encoded proteins. Furthermore, our results highlight a bacteriophage-like nature of early PBCV-1 infection stages, thus implying that this virus uniquely combines bacteriophage-like and eukaryotic-like pathways to accomplish its replication cycle.
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Affiliation(s)
- Elad Milrot
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (EM); (AM)
| | - Eyal Shimoni
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Tali Dadosh
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Katya Rechav
- Chemical Research Support, The Weizmann Institute of Science, Rehovot, Israel
| | - Tamar Unger
- Proteomics, The Weizmann Institute of Science, Rehovot, Israel
| | - James L. Van Etten
- Department of Plant Pathology and Nebraska Center for Virology, University of Nebraska, Lincoln, NE, United States of America
| | - Abraham Minsky
- Department of Structural Biology, The Weizmann Institute of Science, Rehovot, Israel
- * E-mail: (EM); (AM)
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46
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Hosseinizadeh A, Mashayekhi G, Copperman J, Schwander P, Dashti A, Sepehr R, Fung R, Schmidt M, Yoon CH, Hogue BG, Williams GJ, Aquila A, Ourmazd A. Conformational landscape of a virus by single-particle X-ray scattering. Nat Methods 2017; 14:877-881. [PMID: 28805793 DOI: 10.1038/nmeth.4395] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Accepted: 07/05/2017] [Indexed: 11/09/2022]
Abstract
Using a manifold-based analysis of experimental diffraction snapshots from an X-ray free electron laser, we determine the three-dimensional structure and conformational landscape of the PR772 virus to a detector-limited resolution of 9 nm. Our results indicate that a single conformational coordinate controls reorganization of the genome, growth of a tubular structure from a portal vertex and release of the genome. These results demonstrate that single-particle X-ray scattering has the potential to shed light on key biological processes.
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Affiliation(s)
- Ahmad Hosseinizadeh
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Ghoncheh Mashayekhi
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Jeremy Copperman
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Peter Schwander
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Ali Dashti
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Reyhaneh Sepehr
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Russell Fung
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Marius Schmidt
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
| | - Chun Hong Yoon
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Brenda G Hogue
- Biodesign Center for Immunotherapy, Vaccines and Virotherapy, Arizona State University, Tempe, Arizona, USA.,Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, Arizona, USA.,School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | | | - Andrew Aquila
- Linac Coherent Light Source, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Abbas Ourmazd
- Department of Physics, University of Wisconsin-Milwaukee, Milwaukee, Wisconsin, USA
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47
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Nawaz M, Fatima F. Extracellular Vesicles, Tunneling Nanotubes, and Cellular Interplay: Synergies and Missing Links. Front Mol Biosci 2017; 4:50. [PMID: 28770210 PMCID: PMC5513920 DOI: 10.3389/fmolb.2017.00050] [Citation(s) in RCA: 84] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2017] [Accepted: 07/03/2017] [Indexed: 12/15/2022] Open
Abstract
The process of intercellular communication seems to have been a highly conserved evolutionary process. Higher eukaryotes use several means of intercellular communication to address both the changing physiological demands of the body and to fight against diseases. In recent years, there has been an increasing interest in understanding how cell-derived nanovesicles, known as extracellular vesicles (EVs), can function as normal paracrine mediators of intercellular communication, but can also elicit disease progression and may be used for innovative therapies. Over the last decade, a large body of evidence has accumulated to show that cells use cytoplasmic extensions comprising open-ended channels called tunneling nanotubes (TNTs) to connect cells at a long distance and facilitate the exchange of cytoplasmic material. TNTs are a different means of communication to classical gap junctions or cell fusions; since they are characterized by long distance bridging that transfers cytoplasmic organelles and intracellular vesicles between cells and represent the process of heteroplasmy. The role of EVs in cell communication is relatively well-understood, but how TNTs fit into this process is just emerging. The aim of this review is to describe the relationship between TNTs and EVs, and to discuss the synergies between these two crucial processes in the context of normal cellular cross-talk, physiological roles, modulation of immune responses, development of diseases, and their combinatory effects in tissue repair. At the present time this review appears to be the first summary of the implications of the overlapping roles of TNTs and EVs. We believe that a better appreciation of these parallel processes will improve our understanding on how these nanoscale conduits can be utilized as novel tools for targeted therapies.
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Affiliation(s)
- Muhammad Nawaz
- Department of Pathology and Forensic Medicine, Ribeirao Preto Medical School, University of São PauloSão Paulo, Brazil.,Department of Rheumatology and Inflammation Research, Sahlgrenska Academy, University of GothenburgGothenburg, Sweden
| | - Farah Fatima
- Department of Pathology and Forensic Medicine, Ribeirao Preto Medical School, University of São PauloSão Paulo, Brazil
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48
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Galaz-Montoya JG, Ludtke SJ. The advent of structural biology in situ by single particle cryo-electron tomography. BIOPHYSICS REPORTS 2017; 3:17-35. [PMID: 28781998 PMCID: PMC5516000 DOI: 10.1007/s41048-017-0040-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Accepted: 03/30/2017] [Indexed: 01/06/2023] Open
Abstract
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.
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Affiliation(s)
- Jesús G. Galaz-Montoya
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Steven J. Ludtke
- National Center for Macromolecular Imaging, Verna and Marrs McLean Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030 USA
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49
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Tu J, Park T, Morado DR, Hughes KT, Molineux IJ, Liu J. Dual host specificity of phage SP6 is facilitated by tailspike rotation. Virology 2017; 507:206-215. [PMID: 28456019 DOI: 10.1016/j.virol.2017.04.017] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2016] [Revised: 04/13/2017] [Accepted: 04/17/2017] [Indexed: 01/08/2023]
Abstract
Bacteriophage SP6 exhibits dual-host adsorption specificity. The SP6 tailspikes are recognized as important in host range determination but the mechanisms underlying dual host specificity are unknown. Cryo-electron tomography and sub-tomogram classification were used to analyze the SP6 virion with a particular focus on the interaction of tailspikes with host membranes. The SP6 tail is surrounded by six V-shaped structures that interconnect in forming a hand-over-hand hexameric garland. Each V-shaped structure consists of two trimeric tailspike proteins: gp46 and gp47, connected through the adaptor protein gp37. SP6 infection of Salmonella enterica serovars Typhimurium and Newport results in distinguishable changes in tailspike orientation, providing the first direct demonstration how tailspikes can confer dual host adsorption specificity. SP6 also infects S. Typhimurium strains lacking O antigen; in these infections tailspikes have no apparent specific role and the phage tail must therefore interact with a distinct host receptor to allow infection.
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Affiliation(s)
- Jiagang Tu
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Taehyun Park
- Center for Infectious Disease, Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA
| | - Dustin R Morado
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, TX 77030, USA
| | - Kelly T Hughes
- Department of Biology, University of Utah, Salt Lake City, UT 84112, USA
| | - Ian J Molineux
- Center for Infectious Disease, Department of Molecular Biosciences, Institute for Cell and Molecular Biology, University of Texas at Austin, Austin, TX 78712, USA.
| | - Jun Liu
- Department of Pathology and Laboratory Medicine, McGovern Medical School at UTHealth, Houston, TX 77030, USA.
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Demina TA, Pietilä MK, Svirskaitė J, Ravantti JJ, Atanasova NS, Bamford DH, Oksanen HM. HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae. Viruses 2017; 9:v9020032. [PMID: 28218714 PMCID: PMC5332951 DOI: 10.3390/v9020032] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Revised: 01/10/2017] [Accepted: 02/13/2017] [Indexed: 11/16/2022] Open
Abstract
Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1), has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV) in 2016.
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Affiliation(s)
- Tatiana A Demina
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Maija K Pietilä
- Department of Food and Environmental Sciences, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Julija Svirskaitė
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Janne J Ravantti
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Nina S Atanasova
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Dennis H Bamford
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
| | - Hanna M Oksanen
- Department of Biosciences and Institute of Biotechnology, Viikinkaari 9, FIN-00014, University of Helsinki, Helsinki, Finland.
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