172 results on '"David Prangishvili"'
Search Results
2. The structures of two archaeal type IV pili illuminate evolutionary relationships
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Fengbin Wang, Diana P. Baquero, Zhangli Su, Leticia C. Beltran, David Prangishvili, Mart Krupovic, and Edward H. Egelman
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Science - Abstract
Archaeal type IV pili (T4P) mediate adhesion to surfaces and are receptors for hyperthermophilic archaeal viruses. Here, the authors present the cryo-EM structures of two archaeal T4P from Pyrobaculum arsenaticum and Saccharolobus solfataricus and discuss evolutionary relationships between bacterial T4P, archaeal T4P and archaeal flagellar filaments.
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- 2020
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3. Virus-borne mini-CRISPR arrays are involved in interviral conflicts
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Sofia Medvedeva, Ying Liu, Eugene V. Koonin, Konstantin Severinov, David Prangishvili, and Mart Krupovic
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Science - Abstract
Here, the authors investigate the diversity and dynamics of the CRISPRome in the hyperthermophilic archaea of the order Sulfolobales, and find the most abundant spacers to come from mini-CRISPR arrays of archaeal viruses, which might represent a strategy for superinfection exclusion and promotion of archaeal virus speciation.
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- 2019
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4. Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes.
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Ying Liu, Tatiana A Demina, Simon Roux, Pakorn Aiewsakun, Darius Kazlauskas, Peter Simmonds, David Prangishvili, Hanna M Oksanen, and Mart Krupovic
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Biology (General) ,QH301-705.5 - Abstract
The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA (dsDNA) bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families and 3 orders, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counterdefense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered 4 distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine, and anoxic environments.
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- 2021
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5. Structural conservation in a membrane-enveloped filamentous virus infecting a hyperthermophilic acidophile
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Ying Liu, Tomasz Osinski, Fengbin Wang, Mart Krupovic, Stefan Schouten, Peter Kasson, David Prangishvili, and Edward H. Egelman
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Science - Abstract
Only a few archaeal filamentous viruses have been structurally characterized. Here the authors describe the membrane-enveloped Sulfolobus filamentous virus 1 that infects Sulfolobus shibatae and present its 3.7 Å resolution cryo-EM structure, which reveals that major coat proteins are structurally conserved among archaeal filamentous viruses.
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- 2018
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6. Unique architecture of thermophilic archaeal virus APBV1 and its genome packaging
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Denis Ptchelkine, Ashley Gillum, Tomohiro Mochizuki, Soizick Lucas-Staat, Ying Liu, Mart Krupovic, Simon E. V. Phillips, David Prangishvili, and Juha T. Huiskonen
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Science - Abstract
The rod-shaped virus APBV1 is among the most thermostable viruses known. Here, Ptchelkine et al. determine its structure at near-atomic resolution, show that the DNA is packed as left-handed superhelix and identify extended hydrophobic interfaces that likely contribute to the extreme thermostability of the capsid.
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- 2017
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7. Microbial Diversity and Phage–Host Interactions in the Georgian Coastal Area of the Black Sea Revealed by Whole Genome Metagenomic Sequencing
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Ekaterine Jaiani, Ia Kusradze, Tamar Kokashvili, Natia Geliashvili, Nino Janelidze, Adam Kotorashvili, Nato Kotaria, Archil Guchmanidze, Marina Tediashvili, and David Prangishvili
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the Black Sea ,microbial diversity ,phage–host interactions ,metagenomics ,Biology (General) ,QH301-705.5 - Abstract
Viruses have the greatest abundance and highest genetic diversity in marine ecosystems. The interactions between viruses and their hosts is one of the hot spots of marine ecology. Besides their important role in various ecosystems, viruses, especially bacteriophages and their gene pool, are of enormous interest for the development of new gene products with high innovation value. Various studies have been conducted in diverse ecosystems to understand microbial diversity and phage–host interactions; however, the Black Sea, especially the Eastern coastal area, remains among the least studied ecosystems in this regard. This study was aimed at to fill this gap by analyzing microbial diversity and bacteriophage–host interactions in the waters of Eastern Black Sea using a metagenomic approach. To this end, prokaryotic and viral metagenomic DNA from two sampling sites, Poti and Gonio, were sequenced on the Illumina Miseq platform and taxonomic and functional profiles of the metagenomes were obtained using various bioinformatics tools. Our metagenomics analyses allowed us to identify the microbial communities, with Proteobacteria, Cyanobacteria, Actinibacteria, and Firmicutes found to be the most dominant bacterial phyla and Synechococcus and Candidatus Pelagibacter phages found to be the most dominant viral groups in the Black Sea. As minor groups, putative phages specific to human pathogens were identified in the metagenomes. We also characterized interactions between the phages and prokaryotic communities by determining clustered regularly interspaced short palindromic repeats (CRISPR), prophage-like sequences, and integrase/excisionase sequences in the metagenomes, along with identification of putative horizontally transferred genes in the viral contigs. In addition, in the viral contig sequences related to peptidoglycan lytic activity were identified as well. This is the first study on phage and prokaryote diversity and their interactions in the Eastern coastal area of the Black Sea using a metagenomic approach.
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- 2020
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8. Model for a novel membrane envelope in a filamentous hyperthermophilic virus
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Peter Kasson, Frank DiMaio, Xiong Yu, Soizick Lucas-Staat, Mart Krupovic, Stefan Schouten, David Prangishvili, and Edward H Egelman
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archaea ,cryo-electron microscopy ,membranes ,Medicine ,Science ,Biology (General) ,QH301-705.5 - Abstract
Biological membranes create compartments, and are usually formed by lipid bilayers. However, in hyperthermophilic archaea that live optimally at temperatures above 80°C the membranes are monolayers which resemble fused bilayers. Many double-stranded DNA viruses which parasitize such hosts, including the filamentous virus AFV1 of Acidianus hospitalis, are enveloped with a lipid-containing membrane. Using cryo-EM, we show that the membrane in AFV1 is a ~2 nm-thick monolayer, approximately half the expected membrane thickness, formed by host membrane-derived lipids which adopt a U-shaped ‘horseshoe’ conformation. We hypothesize that this unusual viral envelope structure results from the extreme curvature of the viral capsid, as ‘horseshoe’ lipid conformations favor such curvature and host membrane lipids that permit horseshoe conformations are selectively recruited into the viral envelope. The unusual envelope found in AFV1 also has many implications for biotechnology, since this membrane can survive the most aggressive conditions involving extremes of temperature and pH.
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- 2017
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9. Eukaryotic-Like Virus Budding in Archaea
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Emmanuelle R. J. Quemin, Petr Chlanda, Martin Sachse, Patrick Forterre, David Prangishvili, and Mart Krupovic
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Microbiology ,QR1-502 - Abstract
ABSTRACT Similar to many eukaryotic viruses (and unlike bacteriophages), viruses infecting archaea are often encased in lipid-containing envelopes. However, the mechanisms of their morphogenesis and egress remain unexplored. Here, we used dual-axis electron tomography (ET) to characterize the morphogenesis of Sulfolobus spindle-shaped virus 1 (SSV1), the prototype of the family Fuselloviridae and representative of the most abundant archaea-specific group of viruses. Our results show that SSV1 assembly and egress are concomitant and occur at the cellular cytoplasmic membrane via a process highly reminiscent of the budding of enveloped viruses that infect eukaryotes. The viral nucleoprotein complexes are extruded in the form of previously unknown rod-shaped intermediate structures which have an envelope continuous with the host membrane. Further maturation into characteristic spindle-shaped virions takes place while virions remain attached to the cell surface. Our data also revealed the formation of constricted ring-like structures which resemble the budding necks observed prior to the ESCRT machinery-mediated membrane scission during egress of various enveloped viruses of eukaryotes. Collectively, we provide evidence that archaeal spindle-shaped viruses contain a lipid envelope acquired upon budding of the viral nucleoprotein complex through the host cytoplasmic membrane. The proposed model bears a clear resemblance to the egress strategy employed by enveloped eukaryotic viruses and raises important questions as to how the archaeal single-layered membrane composed of tetraether lipids can undergo scission. IMPORTANCE The replication of enveloped viruses has been extensively studied in eukaryotes but has remained unexplored for enveloped viruses infecting Archaea. Here, we provide a sequential view on the assembly and egress of SSV1, a prototypic archaeal virus. The observed process is highly similar to the budding of eukaryotic enveloped viruses, including human immunodeficiency virus, influenza virus, and Ebola virus. The present study is the first to characterize such a phenomenon in archeal cells, showing that membrane budding is not an exclusive feature of eukaryotic viruses. Our results provide significant insights into the biogenesis and architecture of unique, spindle-shaped virions that infect archaea. Furthermore, our findings open doors for future inquiries into (i) the evolution of the virus budding process, (ii) mechanistic details of virus-mediated membrane scission in Archaea, and (iii) elucidation of virus- and host-encoded molecular players responsible for archaeal membrane and surface remodeling.
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- 2016
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10. DNA-Interacting Characteristics of the Archaeal Rudiviral Protein SIRV2_Gp1
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Eveline Peeters, Maarten Boon, Clare Rollie, Ronnie G. Willaert, Marleen Voet, Malcolm F. White, David Prangishvili, Rob Lavigne, and Tessa E.F. Quax
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archaea ,archaeal virus ,Rudiviridae ,SIRV2 ,Sulfolobus ,DNA binding ,helix-turn-helix domain ,Microbiology ,QR1-502 - Abstract
Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rod-shaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally characterize gp1, which is a SIRV2 gene with unknown function. The SIRV2_Gp1 protein is highly expressed during early stages of infection and it is the only protein that is encoded twice on the viral genome. It harbours a helix-turn-helix motif and was therefore hypothesized to bind DNA. The DNA-binding behavior of SIRV2_Gp1 was characterized with electrophoretic mobility shift assays and atomic force microscopy. We provide evidence that the protein interacts with DNA and that it forms large aggregates, thereby causing extreme condensation of the DNA. Furthermore, the N-terminal domain of the protein mediates toxicity to the viral host Sulfolobus. Our findings may lead to biotechnological applications, such as the development of a toxic peptide for the containment of pathogenic bacteria, and add to our understanding of the Rudiviral infection cycle.
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- 2017
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11. Solution structure of an archaeal DNA binding protein with an eukaryotic zinc finger fold.
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Florence Guillière, Chloé Danioux, Carole Jaubert, Nicole Desnoues, Muriel Delepierre, David Prangishvili, Guennadi Sezonov, and J Iñaki Guijarro
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Medicine ,Science - Abstract
While the basal transcription machinery in archaea is eukaryal-like, transcription factors in archaea and their viruses are usually related to bacterial transcription factors. Nevertheless, some of these organisms show predicted classical zinc fingers motifs of the C2H2 type, which are almost exclusively found in proteins of eukaryotes and most often associated with transcription regulators. In this work, we focused on the protein AFV1p06 from the hyperthermophilic archaeal virus AFV1. The sequence of the protein consists of the classical eukaryotic C2H2 motif with the fourth histidine coordinating zinc missing, as well as of N- and C-terminal extensions. We showed that the protein AFV1p06 binds zinc and solved its solution structure by NMR. AFV1p06 displays a zinc finger fold with a novel structure extension and disordered N- and C-termini. Structure calculations show that a glutamic acid residue that coordinates zinc replaces the fourth histidine of the C2H2 motif. Electromobility gel shift assays indicate that the protein binds to DNA with different affinities depending on the DNA sequence. AFV1p06 is the first experimentally characterised archaeal zinc finger protein with a DNA binding activity. The AFV1p06 protein family has homologues in diverse viruses of hyperthermophilic archaea. A phylogenetic analysis points out a common origin of archaeal and eukaryotic C2H2 zinc fingers.
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- 2013
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12. Genomics and genetics of Sulfolobus islandicus LAL14/1, a model hyperthermophilic archaeon
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Carole Jaubert, Chloë Danioux, Jacques Oberto, Diego Cortez, Ariane Bize, Mart Krupovic, Qunxin She, Patrick Forterre, David Prangishvili, and Guennadi Sezonov
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archaea ,sulfolobus islandicus lal14/1 ,genome analysis ,genetics ,crispr ,Biology (General) ,QH301-705.5 - Abstract
The 2 465 177 bp genome of Sulfolobus islandicus LAL14/1, host of the model rudivirus SIRV2, was sequenced. Exhaustive comparative genomic analysis of S. islandicus LAL14/1 and the nine other completely sequenced S. islandicus strains isolated from Iceland, Russia and USA revealed a highly syntenic common core genome of approximately 2 Mb and a long hyperplastic region containing most of the strain-specific genes. In LAL14/1, the latter region is enriched in insertion sequences, CRISPR (clustered regularly interspaced short palindromic repeats), glycosyl transferase genes, toxin–antitoxin genes and MITE (miniature inverted-repeat transposable elements). The tRNA genes of LAL14/1 are preferential targets for the integration of mobile elements but clusters of atypical genes (CAG) are also integrated elsewhere in the genome. LAL14/1 carries five CRISPR loci with 10 per cent of spacers matching perfectly or imperfectly the genomes of archaeal viruses and plasmids found in the Icelandic hot springs. Strikingly, the CRISPR_2 region of LAL14/1 carries an unusually long 1.9 kb spacer interspersed between two repeat regions and displays a high similarity to pING1-like conjugative plasmids. Finally, we have developed a genetic system for S. islandicus LAL14/1 and created ΔpyrEF and ΔCRISPR_1 mutants using double cross-over and pop-in/pop-out approaches, respectively. Thus, LAL14/1 is a promising model to study virus–host interactions and the CRISPR/Cas defence mechanism in Archaea.
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- 2013
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13. Taxonomy proposal 2021: Create 3 new orders and 14 new families in the class Caudoviricetes (Duplodnaviria, Uroviricota) for classification of tailed archaeal viruses
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Ying Liu, Tatiana Demina, Simon Roux, Pakorn Aiewsakun, Kazlauskas, Darius M., Peter Simmonds, David Prangishvili, Oksanen, Hanna M., Mart Krupovic, Molecular and Integrative Biosciences Research Programme, Molecular Principles of Viruses, and Department of Microbiology
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11832 Microbiology and virology - Published
- 2022
14. Egress of archaeal viruses
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David Prangishvili, Junfeng Liu, and Diana P. Baquero
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Archaeal Viruses ,Budding ,viruses ,Immunology ,Virion ,Genome, Viral ,Biology ,biology.organism_classification ,Archaea ,Microbiology ,Genome ,Virus Release ,Virus ,Cell biology ,Cell wall ,Cell membrane ,medicine.anatomical_structure ,Virology ,medicine - Abstract
Viruses of Archaea, arguably the most mysterious part of the virosphere due to their unique morphotypes and genome contents, exploit diverse mechanisms for releasing virus progeny from the host cell. These include virus release as a result of the enzymatic degradation of the cell wall or budding through it, common for viruses of Bacteria and Eukarya, as well as a unique mechanism of virus egress through small polygonal perforations on the cell surface. The process of the formation of these perforations includes the development of pyramidal structures on the membrane of the infected cell, which gradually grow by the expansion of their faces and eventually open like flower petals. This mechanism of virion release is operating exclusively in cells of hyperthermophilic hosts from the phylum Crenarchaeota, which are encased solely by a layer of surface proteins, S-layer. The review focuses on recent developments in understanding structural and biochemical details of all three types of egress mechanisms of archaeal viruses. TAKE AWAYS: Many archaeal viruses exit the host via polygonal perforations on the cell membrane. The molecular mechanism of exit via specific apertures is unique for archaeal viruses. Some enveloped archaeal viruses exploit the budding mechanism for egress.
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- 2021
15. Structural basis of RNA polymerase inhibition by viral and host factors
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Thomas Fouqueau, David Prangishvili, Finn Werner, Dorota Matelska, Natalya Lukoyanova, Luis Miguel Díaz-Santín, Alan C. M. Cheung, Simona Pilotto, Soizick Lucas-Staat, Carol Sheppard, University College of London [London] (UCL), Birkbeck College [University of London], Imperial College London, Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris], Ivane Javakhishvili Tbilisi State University (TSU), University of Bristol [Bristol], Research in the RNAP laboratory at UCL is funded by a Wellcome Investigator Award in Science to FW (WT 207446/Z/17/Z) with the title Mechanisms and Regulation of RNAP transcription., and Institut Pasteur [Paris] (IP)-Université Paris Cité (UPCité)
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Models, Molecular ,Cleavage factor ,Time Factors ,Archaeal Proteins ,Science ,[SDV]Life Sciences [q-bio] ,genetic processes ,Allosteric regulation ,General Physics and Astronomy ,Virus-host interactions ,Article ,Protein Structure, Secondary ,General Biochemistry, Genetics and Molecular Biology ,Viral Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,0302 clinical medicine ,Allosteric Regulation ,Transcription (biology) ,RNA polymerase ,Amino Acid Sequence ,Binding site ,030304 developmental biology ,Host factor ,0303 health sciences ,Multidisciplinary ,biology ,Chemistry ,Cryoelectron Microscopy ,DNA ,DNA-Directed RNA Polymerases ,General Chemistry ,biology.organism_classification ,Viroids ,3. Good health ,Cell biology ,Sulfolobus ,enzymes and coenzymes (carbohydrates) ,Viruses ,health occupations ,Nucleic acid ,bacteria ,Structural biology ,Archaeal biology ,030217 neurology & neurosurgery ,Protein Binding - Abstract
RNA polymerase inhibition plays an important role in the regulation of transcription in response to environmental changes and in the virus-host relationship. Here we present the high-resolution structures of two such RNAP-inhibitor complexes that provide the structural bases underlying RNAP inhibition in archaea. The Acidianus two-tailed virus encodes the RIP factor that binds inside the DNA-binding channel of RNAP, inhibiting transcription by occlusion of binding sites for nucleic acid and the transcription initiation factor TFB. Infection with the Sulfolobus Turreted Icosahedral Virus induces the expression of the host factor TFS4, which binds in the RNAP funnel similarly to eukaryotic transcript cleavage factors. However, TFS4 allosterically induces a widening of the DNA-binding channel which disrupts trigger loop and bridge helix motifs. Importantly, the conformational changes induced by TFS4 are closely related to inactivated states of RNAP in other domains of life indicating a deep evolutionary conservation of allosteric RNAP inhibition., Understanding the structural basis for the inhibition of archaeal eukaryotic-like RNA polymerases (RNAPs) during virus infection is of interest for drug design. Here, the authors present the cryo-EM structures of apo Sulfolobus acidocaldarius RNAP and the RNAP complex structures with two regulatory factors, RIP and TFS4 that inhibit transcription and discuss their inhibitory mechanisms.
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- 2021
16. ICTV Virus Taxonomy Profile: Portogloboviridae
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David Prangishvili, Ying Liu, Mart Krupovic, Institut Pasteur [Paris], Ivane Javakhishvili Tbilisi State University (TSU), Virologie des archées - Archaeal Virology, Production of this summary, the online chapter, and associated resources was funded by a grant from the Wellcome Trust (WT108418AIA), Members of the ICTV Report Consortium are Stuart G. Siddell, Elliot J. Lefkowitz, Sead Sabanadzovic, Peter Simmonds, F. Murilo Zerbini, Donald B. Smith, Richard J. Orton and Mart Krupovic., and Institut Pasteur [Paris] (IP)
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0301 basic medicine ,ORDER SULFOLOBALES ,Portogloboviridae ,viruses ,030106 microbiology ,Biology ,biology.organism_classification ,Genome ,Virology ,3. Good health ,Nucleoprotein ,03 medical and health sciences ,chemistry.chemical_compound ,ICTV ,taxonomy ,030104 developmental biology ,chemistry ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Taxonomy (biology) ,Virus classification ,DNA ,Archaea - Abstract
Portogloboviridae is a family of viruses with circular, double-stranded DNA genomes of about 20 kbp. Their icosahedral virions have a diameter of 87 nm, and consist of an outer protein shell, an inner lipid layer and a nucleoprotein core wound up into a spherical coil. Portogloboviruses infect hyperthermophilic archaea of the genus Saccharolobus , order Sulfolobales and are presumably nonlytic. Portogloboviruses encode mini-CRISPR arrays which they use to compete against other co-infecting viruses. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Portogloboviridae, which is available at ictv.global/report/portogloboviridae.
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- 2021
17. Going to extremes – a metagenomic journey into the dark matter of life
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Alexandra Helleux, Håkon Dahle, Alexander Sczyrba, Karolina Kwiatkowska-Semrau, Anders Svensson, Ruoshi Zhang, Paul Terzian, Olesia Werbowy, Edda Olgudóttir, Gudmundur O. Hreggvidsson, Jonathan Vincent, Andrius Jasilionis, David Prangishvili, Thibaud Mas, Ehmke Pohl, Javier A. Linares-Pastén, Tobias Lutterman, Olafur H. Fridjonsson, Agata Jurczak-Kurek, Martin Steinegger, Arnthor Aevarsson, Justine Vanhalst, Mart Krupovic, Elisabet E. Gudmundsdottir, Sigurlaug Skirnisdottir, Milot Mirdita, Tadeusz Kaczorowski, Monika Szadkowska, Joanna Lange, Magdalena Plotka, Hildegard Watzlawick, François Enault, Magdalena Cichowicz-Cieślak, Sigmar K. Stefansson, Björn Walse, Jessica Louise Ray, Steffen A Lorentsen, Jörn Kalinowski, Slawomir Dabrowski, Josefin Ahlqvist, William Merre, Eric Olo Ndela, Lei Wang, Salam Al-Karadaghi, Sebastian Dorawa, Martin Welin, Francine Perler, Cathrine Pedersen, Tara Róbertsdóttir, Stefanie Freitag-Pohl, Anna-Karina Kaczorowska, Ruth-Anne Sandaa, Jérémy Courtin, Ilmur Jónsdóttir, Ewa Wons, Bjorn T. Adalsteinsson, Úlfur Áugúst Átlasson, Birkir Reynisson, Katrine Stange Overå, Christian Henke, Maria Håkansson, Julien Lebrat, Annika Jochheim, Mathilde Tourigny, Bas Vroling, Ying Liu, Eirin Glomsaker, Olav Lanes, Sigrídur Hjörleifdóttir, Sólveig K Pétursdóttir, Lukasz P. Kozlowski, Bernd Striberny, David Brandt, Agnieszka Morzywolek, Mickael Guérin, Julia Dusaucy, Ida Helene Steen, Clovis Galiez, Sigurd E Gundesø, J. Altenbuchner, Lilja Björk Jónsdóttir, Jørn Remi Henriksen, Katy A. S. Cornish, Tom van den Bergh, Eva Nordberg Karlsson, Johannes Söding, Hördur Gudmundsson, Hasan Arsin, Anita-Elin Fedøy, Emma J Tarrant, Samia Djeffane, Terese Solstad, Matis ohf [Reykjavík], University of Gdańsk (UG), Lund University [Lund], SARomics Biostructures [Lund, Sweden], Universität Stuttgart [Stuttgart], University of Bergen (UiB), Universität Bielefeld = Bielefeld University, Durham University, A&A Biotechnology [Gdansk, Poland], Laboratoire Microorganismes : Génome et Environnement (LMGE), Centre National de la Recherche Scientifique (CNRS)-Université Clermont Auvergne (UCA), Max-Planck-Institut für Biophysikalische Chemie - Max Planck Institute for Biophysical Chemistry [Göttingen], Max-Planck-Gesellschaft, ArcticZymes Technologies [Tromsø, Norway], University of Iceland [Reykjavik], University of Warsaw (UW), Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris] (IP), Bio-Prodict [Nijmegen The Netherlands], Perls of Wisdom Biotech Consulting [Brookline, MA], NORCE Norwegian Research Center, University of Stuttgart, Funding was provided by the Europan Union's Horizon 2020 Research and Innovation Programme Virus-X project: Viral Metagenomics for Innovation Value (grant no. 685778). This work was supported by the BMBF-funded de.NBI Cloud within the German Network for Bioinformatics Infrastructure (de.NBI) (031A537B, 031A533A, 031A538A, 031A533B, 031A535A, 031A537C, 031A534A, 031A532B)., and European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016)
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Engineering ,Exploit ,archaea ,bioprospecting ,Genome, Viral ,virus ,Microbiology ,Viral gene ,03 medical and health sciences ,Viral Proteins ,Hydrothermal Vents ,Databases, Genetic ,Genetics ,Functional studies ,Molecular Biology ,030304 developmental biology ,virosphere ,0303 health sciences ,Bioprospecting ,metagenomics ,030306 microbiology ,business.industry ,Virome ,Scale (chemistry) ,Computational Biology ,Data science ,Europe ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Metagenomics ,Viruses ,Ecosystem dynamics ,business ,thermophiles - Abstract
The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life. © The Author(s) 2021. Published by Oxford University Press on behalf of FEMS.
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- 2021
18. Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes
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Mart Krupovic, Tatiana A. Demina, Hanna M. Oksanen, Ying Liu, Simon Roux, Peter Simmonds, Pakorn Aiewsakun, Darius Kazlauskas, and David Prangishvili
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Comparative genomics ,0303 health sciences ,030306 microbiology ,Archaeal Viruses ,Biology ,biology.organism_classification ,Genome ,Halophile ,Virus ,03 medical and health sciences ,Evolutionary biology ,Taxonomy (biology) ,Gene ,030304 developmental biology ,Archaea - Abstract
The archaeal tailed viruses (arTV), evolutionarily related to tailed double-stranded DNA bacteriophages of the class Caudoviricetes, represent the most common isolates infecting halophilic archaea. Only a handful of these viruses have been genomically characterized, limiting our appreciation of their ecological impacts and evolution. Here, we present 37 new genomes of haloarchaeal tailed virus isolates, more than doubling the current number of sequenced arTVs. Analysis of all 63 available complete genomes of arTVs, which we propose to classify into 14 new families, suggests ancient divergence of archaeal and bacterial tailed viruses and points to an extensive sharing of genes involved in DNA metabolism and counter defense mechanisms, illuminating common strategies of virus-host interactions with tailed bacteriophages. Coupling of the comparative genomics with the host range analysis on a broad panel of haloarchaeal species uncovered four distinct groups of viral tail fiber adhesins controlling the host range expansion. The survey of metagenomes using viral hallmark genes suggests that the global architecture of the arTV community is shaped through recurrent transfers between different biomes, including hypersaline, marine and anoxic environments.
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- 2021
19. Structure and assembly of archaeal viruses
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Diana P, Baquero, Ying, Liu, Fengbin, Wang, Edward H, Egelman, David, Prangishvili, and Mart, Krupovic
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Archaeal Viruses ,Viral Proteins ,Bacteria ,Books ,Virus Assembly ,Capsid Proteins ,Genome, Viral ,Archaea ,Ecosystem ,Phylogeny - Abstract
Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among bacteriophages or viruses of eukaryotes. However, recent environmental studies have shown that archaeal viruses are widespread also in moderate ecosystems, where they play an important ecological role by influencing the turnover of microbial communities, with a global impact on the carbon and nitrogen cycles. In this review, we summarize recent advances in understanding the molecular details of virion organization and assembly of archaeal viruses. We start by briefly introducing the 20 officially recognized families of archaeal viruses and then outline the similarities and differences of archaeal virus assembly with the morphogenesis pathways used by bacterial and eukaryotic viruses, and discuss the evolutionary implications of these observations. Generally, the assembly of the icosahedral archaeal viruses closely follows the mechanisms employed by evolutionarily related bacterial and eukaryotic viruses with the HK97 fold and double jelly-roll major capsid proteins, emphasizing the overall conservation of these pathways over billions of years of evolution. By contrast, archaea-specific viruses employ unique virion assembly mechanisms. We also highlight some of the molecular adaptations underlying the stability of archaeal viruses in extreme environments. Despite considerable progress during the past few years, the archaeal virosphere continues to represent one of the least studied parts of the global virome, with many molecular features awaiting to be discovered and characterized.
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- 2021
20. New insights into the diversity and evolution of the archaeal mobilome from three complete genomes of Saccharolobus shibatae
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Konstantin Severinov, Mart Krupovic, Yoshizumi Ishino, David Prangishvili, Sonoko Ishino, Virginija Cvirkaite-Krupovic, David Brandt, Jörn Kalinowski, Sofia Medvedeva, Ying Liu, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Skolkovo Institute of Science and Technology [Moscow] (Skoltech), Universität Bielefeld = Bielefeld University, Waksman Institute of Microbiology [Piscataway, NJ], Rutgers, The State University of New Jersey [New Brunswick] (RU), Rutgers University System (Rutgers)-Rutgers University System (Rutgers), Institute of Molecular Genetics of National Research Centre «Kurchatov Institute» [Moscow, Russia], Russian Academy of Sciences [Moscow] (RAS), Kyushu University, Ivane Javakhishvili Tbilisi State University (TSU), This work was supported by l’Agence Nationale de la Recherche (Grant ENVIRA, ANR-17-CE15-0005-01) and the Emergence(s) project MEMREMA from Ville de Paris (to M.K.), the European Union’s Horizon 2020 research and innovation program under grant agreement 685778, project VIRUS X (to D.P.and J.K.). Y.L. was a recipient of the Pasteur-Roux-Cantarini Fellowship from Institut Pasteur.S.M.was partly supported by the Metchnikov fellowship from Campus France., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016), Institut Pasteur [Paris], and Kyushu University [Fukuoka]
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0303 health sciences ,biology ,030306 microbiology ,Fuselloviridae ,Lipothrixviridae ,Sequence Analysis, DNA ,biology.organism_classification ,Microbiology ,Genome ,Archaea ,Sulfolobus ,03 medical and health sciences ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Evolutionary biology ,CRISPR ,Humans ,Mobilome ,Mobile genetic elements ,Insertion sequence ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,030304 developmental biology - Abstract
Saccharolobus (formerly Sulfolobus) shibatae B12, isolated from a hot spring in Beppu, Japan in 1982, is one of the first hyperthermophilic and acidophilic archaeal species to be discovered. It serves as a natural host to the extensively studied spindle-shaped virus SSV1, a prototype of the Fuselloviridae family. Two additional Sa. shibatae strains, BEU9 and S38A, sensitive to viruses of the families Lipothrixviridae and Portogloboviridae, respectively, have been isolated more recently. However, none of the strains has been fully sequenced, limiting their utility for studies on archaeal biology and virus-host interactions. Here, we present the complete genome sequences of all three Sa. shibatae strains and explore the rich diversity of their integrated mobile genetic elements (MGE), including transposable insertion sequences, integrative and conjugative elements, plasmids, and viruses, some of which were also detected in the extrachromosomal form. Analysis of related MGEs in other Sulfolobales species and patterns of CRISPR spacer targeting revealed a complex network of MGE distributions, involving horizontal spread and relatively frequent host switching by MGEs over large phylogenetic distances, involving species of the genera Saccharolobus, Sulfurisphaera and Acidianus. Furthermore, we characterize a remarkable case of a virus-to-plasmid transition, whereby a fusellovirus has lost the genes encoding for the capsid proteins, while retaining the replication module, effectively becoming a plasmid. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.
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- 2021
21. A filamentous archaeal virus is enveloped inside the cell and released through pyramidal portals
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Mart Krupovic, David Prangishvili, Diana P. Baquero, Maryse Moya-Nilges, Martin Sachse, Anastasia D. Gazi, Stefan Schouten, Junfeng Liu, Christine Schmitt, Virologie des archées - Archaeal Virology, Université Paris Cité (UPCité)-Microbiologie Intégrative et Moléculaire (UMR6047), Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut Pasteur [Paris] (IP)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Plateforme BioImagerie Ultrastructurale – Ultrastructural BioImaging Platform (UTechS UBI), Institut Pasteur [Paris] (IP), Royal Netherlands Institute for Sea Research (NIOZ), This work was supported by l’Agence Nationale de la Recherche (Grant ANR-17-CE15-0005-01) and Emergence(s) project from Ville de Paris (to M.K.). D.P.B. was part of the Pasteur–Paris University International PhD Program, which has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie Grant Agreement No. 665807. The Unit of Techology & Service Ultrastructural BioImaging is a member facility of France BioImaging (ANR-10-INSB-0004)., We would like to thank Thibault Chaze and Mariette Matondo (Proteomics Platform, Institut Pasteur) for help with the proteomics and Anchelique Mets (Royal Netherlands Institute for Sea Research) for support with lipid analysis. We are also grateful for the helpful discussions and support provided by Jacomine Krijnse-Locker., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), ANR-10-INBS-0004,France-BioImaging,Développment d'une infrastructure française distribuée coordonnée(2010), European Project: 665807,H2020,H2020-MSCA-COFUND-2014,PASTEURDOC(2015), and Institut Pasteur [Paris]
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Cytoplasm ,Electron Microscope Tomography ,Viral protein ,archaeal viruses ,viruses ,virus-associated pyramids ,virus assembly ,medicine.disease_cause ,Virus ,Lipothrixviridae ,Sulfolobus ,Viral Proteins ,03 medical and health sciences ,Viral envelope ,Escherichia coli ,medicine ,030304 developmental biology ,0303 health sciences ,Budding ,Multidisciplinary ,biology ,030306 microbiology ,Saccharolobus ,Virion ,virus egress ,Archaeal Viruses ,Biological Sciences ,biology.organism_classification ,hyperthermophilic archaea ,Cell biology ,Host-Pathogen Interactions ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,cell lysis ,Archaea - Abstract
The majority of viruses infecting hyperthermophilic archaea display unique virion architectures and are evolutionarily unrelated to viruses of bacteria and eukaryotes. The lack of relationships to other known viruses suggests that the mechanisms of virus–host interaction in Archaea are also likely to be distinct. To gain insights into archaeal virus–host interactions, we studied the life cycle of the enveloped, ∼2-μm-longSulfolobus islandicus filamentous virus (SIFV), a member of the family Lipothrixviridae infecting a hyperthermophilic and acidophilic archaeon Saccharolobus islandicus LAL14/1. Using dual-axis electron tomography and convolutional neural network analysis, we characterize the life cycle of SIFV and show that the virions, which are nearly two times longer than the host cell diameter, are assembled in the cell cytoplasm, forming twisted virion bundles organized on a nonperfect hexagonal lattice. Remarkably, our results indicate that envelopment of the helical nucleocapsids takes place inside the cell rather than by budding as in the case of most other known enveloped viruses. The mature virions are released from the cell through large (up to 220 nm in diameter), six-sided pyramidal portals, which are built from multiple copies of a single 89-amino-acid-long viral protein gp43. The overexpression of this protein in Escherichia coli leads to pyramid formation in the bacterial membrane. Collectively, our results provide insights into the assembly and release of enveloped filamentous viruses and illuminate the evolution of virus–host interactions in Archaea.
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- 2021
22. Adnaviria: a New Realm for Archaeal Filamentous Viruses with Linear A-Form Double-Stranded DNA Genomes
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Edward H. Egelman, Diana P. Baquero, Fengbin Wang, Eugene V. Koonin, Valerian V. Dolja, David Prangishvili, Jens H. Kuhn, Mart Krupovic, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), National Institute of Allergy and Infectious Diseases [Bethesda] (NIAID-NIH), National Institutes of Health [Bethesda] (NIH), Department of Biochemistry and Molecular Genetics [Charlottesville], University of Virginia, Department of Botany and Plant Pathology, Oregon State University (OSU), National Library of Medicine (NLM), National Institutes of Health [Bethesda] (NIH)-National Center for Biotechnology Information (NCBI), M.K. was supported by l’Agence Nationale de la Recherche (grant ANR-20-CE20-0009-02) and Emergence(s) project MEMREMA from the Ville de Paris. E.V.K. is supported by the Intramural Research Program of the U.S. National Institutes of Health (National Library of Medicine). E.H.E. was supported by NIH grant R35GM122510. This work was supported in part through a Laulima Government Solutions, LLC, prime contract with the U.S. NIAID under contract no. HHSN272201800013C. J.H.K. performed this work as an employee of Tunnell Government Services (TGS), a subcontractor of Laulima Government Solutions, LLC, under contract no. HHSN272201800013C., ANR-20-CE20-0009,VIROMET,Devoiler le virome des archées methanogenes(2020), Institut Pasteur [Paris], and University of Virginia [Charlottesville]
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viruses ,Immunology ,Rudiviridae ,virus taxonomy ,Microbiology ,Genome ,Lipothrixviridae ,03 medical and health sciences ,Monophyly ,chemistry.chemical_compound ,Virology ,major capsid protein ,virus classification ,Virus classification ,030304 developmental biology ,virus evolution ,0303 health sciences ,International Committee on Taxonomy of Viruses (ICTV) ,Tokiviricetes ,biology ,030306 microbiology ,virus structure and assembly ,Tristromaviridae ,biology.organism_classification ,Ligamenvirales ,hyperthermophilic archaea ,chemistry ,Evolutionary biology ,Insect Science ,Viral evolution ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Commentary ,A-form DNA ,DNA - Abstract
International audience; The International Committee on Taxonomy of Viruses (ICTV) has recently adopted a comprehensive, hierarchical system of virus taxa. The highest ranks in this hierarchy are realms, each of which is considered monophyletic but apparently originated independently of other realms. Here, we announce the creation of a new realm, Adnaviria, which unifies archaeal filamentous viruses with linear A-form double-stranded DNA genomes and characteristic major capsid proteins unrelated to those encoded by other known viruses.
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- 2021
23. Microbial Diversity and Phage-Host Interactions in the Georgian Coastal Area of the Black Sea Revealed by Whole Genome Metagenomic Sequencing
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Archil Guchmanidze, Tamar Kokashvili, Ia Kusradze, Nato Kotaria, Natia Geliashvili, Adam Kotorashvili, David Prangishvili, E. Jaiani, Marina Tediashvili, and Nino Janelidze
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DNA, Bacterial ,Firmicutes ,viruses ,Pharmaceutical Science ,Genome, Viral ,Genome ,Article ,03 medical and health sciences ,Drug Discovery ,CRISPR ,Bacteriophages ,Pharmacology, Toxicology and Pharmaceutics (miscellaneous) ,lcsh:QH301-705.5 ,Ecosystem ,030304 developmental biology ,0303 health sciences ,Genetic diversity ,metagenomics ,the Black Sea ,biology ,Bacteria ,Whole Genome Sequencing ,030306 microbiology ,Microbiota ,Prokaryote ,respiratory system ,phage–host interactions ,biology.organism_classification ,lcsh:Biology (General) ,Black Sea ,Evolutionary biology ,Metagenomics ,microbial diversity ,DNA, Viral ,Host-Pathogen Interactions ,Metagenome ,Gene pool ,Proteobacteria ,Water Microbiology ,human activities ,Genome, Bacterial - Abstract
Viruses have the greatest abundance and highest genetic diversity in marine ecosystems. The interactions between viruses and their hosts is one of the hot spots of marine ecology. Besides their important role in various ecosystems, viruses, especially bacteriophages and their gene pool, are of enormous interest for the development of new gene products with high innovation value. Various studies have been conducted in diverse ecosystems to understand microbial diversity and phage&ndash, host interactions, however, the Black Sea, especially the Eastern coastal area, remains among the least studied ecosystems in this regard. This study was aimed at to fill this gap by analyzing microbial diversity and bacteriophage&ndash, host interactions in the waters of Eastern Black Sea using a metagenomic approach. To this end, prokaryotic and viral metagenomic DNA from two sampling sites, Poti and Gonio, were sequenced on the Illumina Miseq platform and taxonomic and functional profiles of the metagenomes were obtained using various bioinformatics tools. Our metagenomics analyses allowed us to identify the microbial communities, with Proteobacteria, Cyanobacteria, Actinibacteria, and Firmicutes found to be the most dominant bacterial phyla and Synechococcus and Candidatus Pelagibacter phages found to be the most dominant viral groups in the Black Sea. As minor groups, putative phages specific to human pathogens were identified in the metagenomes. We also characterized interactions between the phages and prokaryotic communities by determining clustered regularly interspaced short palindromic repeats (CRISPR), prophage-like sequences, and integrase/excisionase sequences in the metagenomes, along with identification of putative horizontally transferred genes in the viral contigs. In addition, in the viral contig sequences related to peptidoglycan lytic activity were identified as well. This is the first study on phage and prokaryote diversity and their interactions in the Eastern coastal area of the Black Sea using a metagenomic approach.
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- 2020
24. Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments
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Edward H. Egelman, Fengbin Wang, Leticia C. Beltran, Zhangli Su, David Prangishvili, Tomasz Osinski, Diana P. Baquero, Mart Krupovic, Weili Zheng, University of Virginia [Charlottesville], Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], This work was supported by NIH Grant R35GM122510 (E.H.E.). M.K. was supported by l’Agence Nationale de la Recherche Grant ANR-17-CE15-0005-01. D.P.B. is part of the Pasteur–Paris University International PhD Program, which has received funding from the European Union’s Horizon 2020 Research and Innovation Programme under Marie Sklodowska-Curie Grant Agreement 665807., Imaging of SSRV1 was performed at the National Cancer Institute’s National Cryo-EM Facility at the Frederick National Laboratory for Cancer Research under Contract HSSN261200800001E. Imaging of SIFV was done at the Molecular Electron Microscopy Core Facility at the University of Virginia, which is supported by the School of Medicine, We thank Thibault Chaze and Mariette Matondo (Pasteur Proteomics Platform) for help with the mass spectrometry analyses., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), European Project: 665807,H2020,H2020-MSCA-COFUND-2014,PASTEURDOC(2015), University of Virginia, and Institut Pasteur [Paris] (IP)
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Archaeal Viruses ,viruses ,Genome, Viral ,Genome ,Virus ,Sulfolobus ,03 medical and health sciences ,chemistry.chemical_compound ,Capsid ,Viral envelope ,Phylogeny ,extremophiles ,030304 developmental biology ,Genetics ,0303 health sciences ,Multidisciplinary ,030306 microbiology ,Chemistry ,[SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE] ,DNA Viruses ,Protein superfamily ,Biological Sciences ,Biological Evolution ,hyperthermophilic archaea ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,Viral evolution ,DNA, Viral ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,cryo-EM ,DNA ,Sulfolobales ,filamentous viruses ,Extreme Environments - Abstract
International audience; Living organisms expend metabolic energy to repair and maintain their genomes, while viruses protect their genetic material by completely passive means. We have used cryo-electron microscopy (cryo-EM) to solve the atomic structures of two filamentous double-stranded DNA viruses that infect archaeal hosts living in nearly boiling acid: Saccharolobus solfataricus rod-shaped virus 1 (SSRV1), at 2.8-Å resolution, and Sulfolobus islandicus filamentous virus (SIFV), at 4.0-Å resolution. The SIFV nucleocapsid is formed by a heterodimer of two homologous proteins and is membrane enveloped, while SSRV1 has a nucleocapsid formed by a homo-dimer and is not enveloped. In both, the capsid proteins wrap around the DNA and maintain it in an A-form. We suggest that the A-form is due to both a nonspecific desolvation of the DNA by the protein, and a specific coordination of the DNA phosphate groups by positively charged residues. We extend these observations by comparisons with four other archaeal filamentous viruses whose structures we have previously determined, and show that all 10 capsid proteins (from four heterodimers and two homo-dimers) have obvious structural homology while sequence similarity can be nonexistent. This arises from most capsid residues not being under any strong selective pressure. The inability to detect homology at the sequence level arises from the sampling of viruses in this part of the biosphere being extremely sparse. Comparative structural and genomic analyses suggest that nonenvel-oped archaeal viruses have evolved from enveloped viruses by shedding the membrane, indicating that this trait may be relatively easily lost during virus evolution. cryo-EM | extremophiles | hyperthermophilic archaea | filamentous viruses
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- 2020
25. Structure of a filamentous virus uncovers familial ties within the archaeal virosphere
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Diana P. Baquero, Edward H. Egelman, Zhangli Su, David Prangishvili, Tomasz Osinski, Mart Krupovic, Fengbin Wang, Department of Biochemistry and Molecular Genetics [Charlottesville], University of Virginia [Charlottesville], Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Collège doctoral [Sorbonne universités], Sorbonne Université (SU), Ivane Javakhishvili Tbilisi State University (TSU), This work was supported by the National Institute of General Medical Sciences (GM122510 to E.H.E.), the European Union’s Horizon 2020 Research and Innovation Program (685778, project VIRUS X to D.P.), and l’Agence Nationale de la Recherche (ANR-17-CE15-0005-01 to M.K.). D.P.B. is part of the Pasteur—Paris University (PPU) International PhD Program, which has received funding from the European Union’s Horizon 2020 research and innovation program under the Marie Sklodowska-Curie grant agreement no. 665807., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016), University of Virginia, Institut Pasteur [Paris] (IP), and Collège Doctoral
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virus evolution ,Genetics ,0303 health sciences ,030306 microbiology ,[SDV]Life Sciences [q-bio] ,viruses ,Lineage (evolution) ,Archaeal Viruses ,Biology ,hyperthermophilic archaea ,Microbiology ,Genome ,Virus ,03 medical and health sciences ,Capsid ,Virology ,Viral evolution ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,cryo-EM ,Human virome ,virus structure ,Rapid Communication ,Virus classification ,major capsid proteins ,030304 developmental biology - Abstract
Viruses infecting hyperthermophilic archaea represent one of the most enigmatic parts of the global virome, with viruses from different families showing no genomic relatedness to each other or to viruses of bacteria and eukaryotes. Tristromaviruses, which build enveloped filamentous virions and infect hyperthermophilic neutrophiles of the order Thermoproteales, represent one such enigmatic virus families. They do not share genes with viruses from other families and have been believed to represent an evolutionarily independent virus lineage. A cryo-electron microscopic reconstruction of the tristromavirus Pyrobaculum filamentous virus 2 at 3.4 Å resolution shows that the virion is constructed from two paralogous major capsid proteins (MCP) which transform the linear dsDNA genome of the virus into A-form by tightly wrapping around it. Unexpectedly, the two MCP are homologous to the capsid proteins of other filamentous archaeal viruses, uncovering a deep evolutionary relationship within the archaeal virosphere.
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- 2020
26. Virus-borne mini-CRISPR arrays are involved in interviral conflicts
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Ying Liu, Sofia Medvedeva, Eugene V. Koonin, Mart Krupovic, David Prangishvili, Konstantin Severinov, Skolkovo Institute of Science and Technology [Moscow] (Skoltech), Sorbonne Université (SU), Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris], National Institutes of Health [Bethesda] (NIH), Ivane Javakhishvili Tbilisi State University (TSU), Institut Pasteur [Paris] (IP), Virologie des archées - Archaeal Virology, ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), and European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016)
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0301 basic medicine ,Archaeal Viruses ,Genome evolution ,CRISPR-Cas systems ,Science ,viruses ,[SDV]Life Sciences [q-bio] ,030106 microbiology ,Population ,General Physics and Astronomy ,Genome, Viral ,Superinfection exclusion ,General Biochemistry, Genetics and Molecular Biology ,Virus ,CRISPR Spacers ,Article ,Evolution, Molecular ,03 medical and health sciences ,CRISPR ,Clustered Regularly Interspaced Short Palindromic Repeats ,education ,lcsh:Science ,Phylogeny ,Genetics ,education.field_of_study ,Multidisciplinary ,biology ,Base Sequence ,General Chemistry ,biology.organism_classification ,Archaea ,030104 developmental biology ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,lcsh:Q ,Sulfolobales - Abstract
CRISPR-Cas immunity is at the forefront of antivirus defense in bacteria and archaea and specifically targets viruses carrying protospacers matching the spacers catalogued in the CRISPR arrays. Here, we perform deep sequencing of the CRISPRome—all spacers contained in a microbiome—associated with hyperthermophilic archaea of the order Sulfolobales recovered directly from an environmental sample and from enrichment cultures established in the laboratory. The 25 million CRISPR spacers sequenced from a single sampling site dwarf the diversity of spacers from all available Sulfolobales isolates and display complex temporal dynamics. Comparison of closely related virus strains shows that CRISPR targeting drives virus genome evolution. Furthermore, we show that some archaeal viruses carry mini-CRISPR arrays with 1–2 spacers and preceded by leader sequences but devoid of cas genes. Closely related viruses present in the same population carry spacers against each other. Targeting by these virus-borne spacers represents a distinct mechanism of heterotypic superinfection exclusion and appears to promote archaeal virus speciation., Here, the authors investigate the diversity and dynamics of the CRISPRome in the hyperthermophilic archaea of the order Sulfolobales, and find the most abundant spacers to come from mini-CRISPR arrays of archaeal viruses, which might represent a strategy for superinfection exclusion and promotion of archaeal virus speciation.
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- 2019
27. New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities
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Ying Liu, David Prangishvili, Simonetta Bartolucci, Mart Krupovic, Patrizia Contursi, Virginija Cvirkaite-Krupovic, Monica Piochi, Diana P. Baquero, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris] (IP), Collège Doctoral, Sorbonne Université (SU), University of Naples Federico II = Università degli studi di Napoli Federico II, Istituto Nazionale di Geofisica e Vulcanologia - Sezione di Napoli (INGV), Istituto Nazionale di Geofisica e Vulcanologia, Ivane Javakhishvili Tbilisi State University (TSU), This work was supported by l’Agence Nationale de la Recherche (France) project ENVIRA (to M.K.) and the European Union’s Horizon 2020 research and innovation program under grant agreement 685778, project VIRUS X (to D.P.). Y.L. is a recipient of the Pasteur-Roux-Cantarini Fellowship from Institut Pasteur. D.P.B. is part of the Pasteur—Paris University (PPU) International PhD Program, which has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 665807., We are also grateful to the Ultrastructural BioImaging (UTechS UBI) unit of Institut Pasteur for access to electron microscopes and Marc Monot from the Biomics Platform of Institut Pasteur for helpful discussions on genome assembly., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), Institut Pasteur [Paris], Collège doctoral [Sorbonne universités], University of Naples Federico II, Baquero, Dp, Contursi, P, Piochi, M, Bartolucci, S, Liu, Y, Cvirkaite-Krupovic, V, Prangishvili, D, and Krupovic, M.
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Archaeal Viruses ,viruses ,Rudiviridae ,Genome, Viral ,Microbiology ,Article ,03 medical and health sciences ,Monophyly ,Virology ,Humans ,Human virome ,Clade ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,0303 health sciences ,biology ,030306 microbiology ,DNA Viruses ,biology.organism_classification ,Archaea ,Italy ,Evolutionary biology ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Viruses ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Rudivirus ,Metallosphaera ,Acidianus - Abstract
Viruses of hyperthermophilic archaea represent one of the least understood parts of the virosphere, showing little genomic and morphological similarity to viruses of bacteria or eukaryotes. Here, we investigated virus diversity in the active sulfurous fields of the Campi Flegrei volcano in Pozzuoli, Italy. Virus-like particles displaying eight different morphotypes, including lemon-shaped, droplet-shaped and bottle-shaped virions, were observed and five new archaeal viruses proposed to belong to familiesRudiviridae,GlobuloviridaeandTristromaviridaewere isolated and characterized. Two of these viruses infect neutrophilic hyperthermophiles of the genusPyrobaculum, whereas the remaining three have rod-shaped virions typical of the familyRudiviridaeand infect acidophilic hyperthermophiles belonging to three different genera of the order Sulfolobales, namely,Saccharolobus,AcidianusandMetallosphaera. Notably,Metallosphaerarod-shaped virus 1 is the first rudivirus isolated onMetallosphaeraspecies. Phylogenomic analysis of the newly isolated and previously sequenced rudiviruses revealed a clear biogeographic pattern, with all Italian rudiviruses forming a monophyletic clade, suggesting geographical structuring of virus communities in extreme geothermal environments. Furthermore, we propose a revised classification of theRudiviridaefamily, with establishment of five new genera. Collectively, our results further show that high-temperature continental hydrothermal systems harbor a highly diverse virome and shed light on the evolution of archaeal viruses.
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- 2019
28. ICTV Virus Taxonomy Profile: Clavaviridae
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David Prangishvili, Mart Krupovic, Tomohiro Mochizuki, Ying Liu, Virologie des archées - Archaeal Virology, Institut Pasteur [Paris], Earth-Life Science Institute [Tokyo] (ELSI), Tokyo Institute of Technology [Tokyo] (TITECH), Production of this summary, the online chapter, and associated resources was funded by a grant from the Wellcome Trust (WT108418AIA)., Members of the ICTV (10th) Report Consortium are Elliot J. Lefkowitz, Andrew J. Davison, Stuart G. Siddell, Peter Simmonds, Sead Sabanadzovic, Donald B. Smith, Richard J. Orton and Andrew M. Kropinski., and Institut Pasteur [Paris] (IP)
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0301 basic medicine ,MESH: Virus Replication/physiology ,Aeropyrum ,viruses ,030106 microbiology ,MESH: Aeropyrum/virology ,Genome ,Virus ,MESH: Viruses, Unclassified/classification ,MESH: Viruses, Unclassified/genetics ,03 medical and health sciences ,taxonomy ,MESH: Genome, Viral ,Virology ,ICTV Report ,Aeropyrum pernix ,Clavaviridae ,Virus classification ,biology ,Superhelix ,biology.organism_classification ,030104 developmental biology ,Capsid ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Clavaviridae 001295 - Abstract
International audience; The family Clavaviridae includes viruses that replicate in hyperthermophilic archaea from the genus Aeropyrum. The non-enveloped rigid virions are rod-shaped, with dimensions of about 143×16 nm, and have terminal cap structures, one of which is pointed and carries short fibres, while the other is rounded. The virion displays helical symmetry and is constructed from a single major α-helical protein, which is heavily glycosylated, and several minor capsid proteins. The 5278 bp, circular, double-stranded DNA genome of Aeropyrum pernix bacilliform virus 1 is packed inside the virion as a left-handed superhe-lix. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Clavaviridae, which is available at www. ictv. global/ report/ clavaviridae.
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- 2019
29. An extensively glycosylated archaeal pilus survives extreme conditions
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Tomasz Osinski, David Prangishvili, Edward H. Egelman, Nicholas E. Sherman, Joseph S. Wall, Virginija Cvirkaite-Krupovic, Frank DiMaio, Zhangli Su, Mart Krupovic, Fengbin Wang, Mark A. B. Kreutzberger, Guilherme A. P. de Oliveira, University of Virginia [Charlottesville], Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Department of Biochemistry [Washington ], University of Washington [Seattle], Brookhaven National Laboratory [Upton, NY] (BNL), U.S. Department of Energy [Washington] (DOE)-UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), State University of New York (SUNY)-State University of New York (SUNY), This work was supported by NIH grants GM122510 (to E.H.E.) and GM123089 (to F.D.), as well as l’Agence Nationale de la Recherche project ENVIRA (ANR-17-CE15-0005-01 to M.K.). M.A.B.K. was supported by NIH grant T32 GM080186. The cryo-EM imaging conducted at the Molecular Electron Microscopy Core facility at the University of Virginia was supported by the School of Medicine and built with NIH grant G20-RR31199. The Titan Krios and Falcon II direct electron detectors were obtained with NIH grants S10-RR025067 and S10-OD018149, respectively., We thank V. Conticello for the suggestion of TFMS. We are also grateful to the Ultrastructural BioImaging (UTechS UBI) unit of Institut Pasteur for access to electron microscopes., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), University of Virginia, Institut Pasteur [Paris] (IP), UT-Battelle, LLC-Stony Brook University [SUNY] (SBU), and State University of New York (SUNY)-State University of New York (SUNY)-U.S. Department of Energy [Washington] (DOE)
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Models, Molecular ,MESH: Archaea/cytology ,MESH: Fimbriae Proteins/chemistry ,Glycosylation ,Protein Conformation ,MESH: Sequence Analysis, Protein ,MESH: Trypsin ,Applied Microbiology and Biotechnology ,Pilus ,MESH: Fimbriae Proteins/ultrastructure ,Serine ,chemistry.chemical_compound ,MESH: Protein Conformation ,Sequence Analysis, Protein ,Trypsin ,Threonine ,Guanidine ,0303 health sciences ,biology ,Protein Stability ,Chemistry ,MESH: Hydrophobic and Hydrophilic Interactions ,MESH: Archaeal Proteins/chemistry ,Archaeal Viruses ,MESH: Glycosylation ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,MESH: Pepsin A ,Fimbriae Proteins ,MESH: Cryoelectron Microscopy ,Hydrophobic and Hydrophilic Interactions ,MESH: Models, Molecular ,Microbiology (medical) ,MESH: Archaea/metabolism ,Archaeal Proteins ,Immunology ,Microbiology ,Article ,Sulfolobus ,Applied microbiology ,03 medical and health sciences ,MESH: Sulfolobus/cytology ,MESH: Protein Stability ,Genetics ,MESH: Fimbriae Proteins/metabolism ,MESH: Sulfolobus/chemistry ,030304 developmental biology ,MESH: Sulfolobus/metabolism ,MESH: Archaeal Proteins/ultrastructure ,030306 microbiology ,Cryoelectron Microscopy ,MESH: Archaea/growth & development ,Cell Biology ,Archaea ,Pepsin A ,13. Climate action ,Pilin ,biology.protein ,Biophysics ,Flagellin ,MESH: Archaeal Proteins/metabolism - Abstract
Pili on the surface of Sulfolobus islandicus are used for many functions, and serve as receptors for certain archaeal viruses. The cells grow optimally at pH 3 and ~80 °C, exposing these extracellular appendages to a very harsh environment. The pili, when removed from cells, resist digestion by trypsin or pepsin, and survive boiling in sodium dodecyl sulfate or 5 M guanidine hydrochloride. We used electron cryo-microscopy to determine the structure of these filaments at 4.1 A resolution. An atomic model was built by combining the electron density map with bioinformatics without previous knowledge of the pilin sequence—an approach that should prove useful for assemblies where all of the components are not known. The atomic structure of the pilus was unusual, with almost one-third of the residues being either threonine or serine, and with many hydrophobic surface residues. While the map showed extra density consistent with glycosylation for only three residues, mass measurements suggested extensive glycosylation. We propose that this extensive glycosylation renders these filaments soluble and provides the remarkable structural stability. We also show that the overall fold of the archaeal pilin is remarkably similar to that of archaeal flagellin, establishing common evolutionary origins. The electron cryo-microscopy structure of Sulfolobus islandicus pili enabled the identification of SiL_2606 as the main pilin in these filaments and revealed that the pili are glycosylated, which probably explains how these structures remain soluble and stable even when cells grow at pH 3 and 80 °C.
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- 2019
30. Novel haloarchaeal viruses from Lake Retba infecting Haloferax and Halorubrum species
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Bina Prajapati, Mart Krupovic, Télesphore Sime-Ngando, Carolina Megumi Mizuno, Patrik Forterre, Hanna M. Oksanen, David Prangishvili, Soizick Lucas-Staat, Dennis H. Bamford, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Helsingin yliopisto = Helsingfors universitet = University of Helsinki, Laboratoire Microorganismes : Génome et Environnement (LMGE), Université Clermont Auvergne [2017-2020] (UCA [2017-2020])-Centre National de la Recherche Scientifique (CNRS), This work was partly supported by Agence Nationale pour la Recherche grant #ANR‐17‐CE15‐0005‐01 (project ENVIRA) to MK and the European Research Council (ERC) grant from the European Union's Seventh Framework Program (FP/2007‐2013)/Project EVOMOBIL‐ERC Grant Agreement no. 340440 to PF. CMM was supported by the European Molecular Biology Organization (ALTF 1562‐2015) and Marie Curie Actions program from the European Commission (LTFCOFUND2013, GA‐2013‐609409)., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), European Project: 340440,EC:FP7:ERC,ERC-2013-ADG,EVOMOBIL(2014), European Project: 609409,EC:FP7:PEOPLE,FP7-PEOPLE-2013-COFUND,LTFCOFUND2013(2014), Institut Pasteur [Paris], University of Helsinki, Molecular and Integrative Biosciences Research Programme, Structure of the Viral Universe, Molecular Principles of Viruses, and Aerovirology Research Group
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viruses ,BACTERIOPHAGES ,Microbiology ,Genome ,Virus ,03 medical and health sciences ,MULTIPLE SEQUENCE ALIGNMENT ,Caudovirales ,EVOLUTIONARY HISTORY ,PLEOMORPHIC VIRUSES ,Phylogenetics ,Haloferax ,HYPERSALINE ENVIRONMENTS ,Halorubrum ,Ecology, Evolution, Behavior and Systematics ,Phylogeny ,1183 Plant biology, microbiology, virology ,030304 developmental biology ,Genetics ,0303 health sciences ,biology ,030306 microbiology ,ARCHAEAL VIRUSES ,Virion ,DNA-REPLICATION ,Archaeal Viruses ,biology.organism_classification ,VIRION ARCHITECTURE ,Senegal ,GENOME ,Lakes ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Metagenome ,TAILED VIRUSES ,Archaea - Abstract
International audience; The diversity of archaeal viruses is severely undersampled compared with that of viruses infecting bacteria and eukaryotes, limiting our understanding on their evolution and environmental impacts. Here, we describe the isolation and characterization of four new viruses infecting halophilic archaea from the saline Lake Retba, located close to Dakar on the coast of Senegal. Three of the viruses, HRPV10, HRPV11 and HRPV12, have enveloped pleomorphic virions and should belong to the family Pleolipoviridae, whereas the forth virus, HFTV1, has an icosahedral capsid and a long non-contractile tail, typical of bacterial and archaeal members of the order Caudovirales. Comparative genomic and phylogenomic analyses place HRPV10, HRPV11 and HRPV12 into the genus Betapleolipovirus, whereas HFTV1 appears to be most closely related to the unclassified Halorubrum virus HRTV-4. Differently from HRTV-4, HFTV1 encodes host-derived minichromosome maintenance helicase and PCNA homologues, which are likely to orchestrate its genome replication. HFTV1, the first archaeal virus isolated on a Haloferax strain, could also infect Halorubrum sp., albeit with an eightfold lower efficiency, whereas pleolipoviruses nearly exclusively infected autochthonous Halorubrum strains. Mapping of the metagenomic sequences from this environment to the genomes of isolated haloarchaeal viruses showed that these known viruses are underrepresented in the available viromes.
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- 2019
31. New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures
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Jörn Kalinowski, Sonoko Ishino, Yoshizumi Ishino, David Prangishvili, Mart Krupovic, David Brandt, Eugene V. Koonin, Ying Liu, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Universität Bielefeld, Kyushu University, National Center for Biotechnology Information (NCBI), This work was supported by the European Union's Horizon 2020 research and innovation program under grant agreement 685778 (project VIRUS‐X), and l'Agence Nationale de la Recherche (projects EXAVIR and ENVIRA)., ANR-13-BSV3-0017,EXAVIR,Exit and assembly of hyperthermophilic archaeal viruses(2013), ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016), Institut Pasteur [Paris], and Kyushu University [Fukuoka]
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Archaeal Viruses ,[SDV]Life Sciences [q-bio] ,viruses ,Rudiviridae ,Genome, Viral ,Biology ,Virus Replication ,Microbiology ,Hot Springs ,Virus ,Lipothrixviridae ,03 medical and health sciences ,Japan ,Bacteriophages ,Human virome ,Phylogeny ,Ecology, Evolution, Behavior and Systematics ,030304 developmental biology ,Genetics ,0303 health sciences ,030306 microbiology ,DNA virus ,biology.organism_classification ,Archaea ,Viral replication ,Metagenomics ,Metagenome - Abstract
International audience; Viruses infecting hyperthermophilic archaea of the phylum Crenarchaeota display enormous morphological and genetic diversity, and are classified into 12 families. Eight of these families include only one or two species, indicating sparse sampling of the crenarchaeal virus diversity. In an attempt to expand the crenarchaeal virome, we explored virus diversity in the acidic, hot spring Umi Jigoku in Beppu, Japan. Environmental samples were used to establish enrichment cultures under conditions favouring virus replication. The host diversity in the enrichment cultures was restricted to members of the order Sulfolobales. Metagenomic sequencing of the viral communities yielded seven complete or near-complete double-stranded DNA virus genomes. Six of these genomes could be attributed to polyhedral and filamentous viruses that were observed by electron microscopy in the enrichment cultures. Two icosahedral viruses represented species in the family Portogloboviridae. Among the filamentous viruses, two were identified as new species in the families Rudiviridae and Lipothrixviridae, whereas two other formed a group seemingly distinct from the known virus genera. No particle morphotype could be unequivocally assigned to the seventh viral genome, which apparently represents a new virus type. Our results suggest that filamentous viruses are globally distributed and are prevalent virus types in extreme geothermal environments.
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- 2019
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32. Integrated mobile genetic elements in Thaumarchaeota
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Mart Krupovic, Sofia Medvedeva, Patrick Forterre, Kira S. Makarova, Yuri I. Wolf, Eugene V. Koonin, David Prangishvili, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), National Center for Biotechnology Information (NCBI), Skolkovo Institute of Science and Technology - Skoltech (RUSSIA), Collège Doctoral, Sorbonne Université (SU), Institut de Biologie Intégrative de la Cellule (I2BC), Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), This work was supported by the European Union's Horizon 2020 research and innovation program under grant agreement 685778 (project VIRUS‐X), l'Agence Nationale de la Recherche (project ENVIRA, #ANR‐17‐CE15‐0005‐01) and European Research Council (ERC) grant from the European Union's Seventh Framework Program (FP/2007‐2013)/Project EVOMOBIL‐ERC Grant Agreement no. 340440. Y.I.W., K.S.M. and E.V.K. are supported through the intramural program of the U.S. National Institutes of Health. S.M. was supported by Vernadski fellowship from Campus France, RSF 14‐14‐00988 and Skoltech SBI program grant to Konstantin Severinov., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016), European Project: 340440,EC:FP7:ERC,ERC-2013-ADG,EVOMOBIL(2014), Institut Pasteur [Paris], Collège doctoral [Sorbonne universités], Sorbonne Universités, Institute for Integrative Biology of the Cell, and Commissariat à l'énergie atomique et aux énergies alternatives (CEA)-Centre National de la Recherche Scientifique (CNRS)-Université Paris-Saclay
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Transposable element ,Thaumarchaeota ,Archaeal Proteins ,Biology ,Microbiology ,Genome ,03 medical and health sciences ,Plasmid ,Caudovirales ,Gene ,Ecology, Evolution, Behavior and Systematics ,Research Articles ,Phylogeny ,030304 developmental biology ,Genetics ,0303 health sciences ,030306 microbiology ,biology.organism_classification ,Archaea ,DNA Transposable Elements ,Mobilome ,Mobile genetic elements ,CRISPR-Cas Systems ,[SDE.BE]Environmental Sciences/Biodiversity and Ecology ,Oxidoreductases ,Research Article ,Plasmids - Abstract
International audience; To explore the diversity of mobile genetic elements (MGE) associated with archaea of the phylum Thaumarchaeota, we exploited the property of most MGE to integrate into the genomes of their hosts. Integrated MGE (iMGE) were identified in 20 thaumarchaeal genomes amounting to 2 Mbp of mobile thaumarchaeal DNA. These iMGE group into five major classes: (i) proviruses, (ii) casposons, (iii) insertion sequence‐like transposons, (iv) integrative‐conjugative elements and (v) cryptic integrated elements. The majority of the iMGE belong to the latter category and might represent novel families of viruses or plasmids. The identified proviruses are related to tailed viruses of the order Caudovirales and to tailless icosahedral viruses with the double jelly‐roll capsid proteins. The thaumarchaeal iMGE are all connected within a gene sharing network, highlighting pervasive gene exchange between MGE occupying the same ecological niche. The thaumarchaeal mobilome carries multiple auxiliary metabolic genes, including multicopper oxidases and ammonia monooxygenase subunit C (AmoC), and stress response genes, such as those for universal stress response proteins (UspA). Thus, iMGE might make important contributions to the fitness and adaptation of their hosts. We identified several iMGE carrying type I‐B CRISPR‐Cas systems and spacers matching other thaumarchaeal iMGE, suggesting antagonistic interactions between coexisting MGE and symbiotic relationships with the ir archaeal hosts.
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- 2019
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33. ICTV Virus Taxonomy Profile: Tristromaviridae
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David, Prangishvili, Elena, Rensen, Tomohiro, Mochizuki, Mart, Krupovic, Ictv Report Consortium, Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris], Département de Biologie cellulaire et infection - Department of Cell Biology and infection (BCI), Tokyo Institute of Technology [Tokyo] (TITECH), Production of this summary, the online chapter, and associated resources was funded by a grant from the Wellcome Trust (WT108418AIA)., Members of the ICTV 10th Report Consortium are Elliot J. Lefkowitz, Andrew J. Davison, Stuart G. Siddell, Peter Simmonds, Sead Sabanadzovic, Donald B. Smith, Richard J. Orton and Andrew M. Kropinski., and Institut Pasteur [Paris] (IP)
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0301 basic medicine ,viruses ,[SDV]Life Sciences [q-bio] ,030106 microbiology ,[SDV.BID.SPT]Life Sciences [q-bio]/Biodiversity/Systematics, Phylogenetics and taxonomy ,Thermoproteales ,Genome ,03 medical and health sciences ,chemistry.chemical_compound ,taxonomy ,Virology ,ICTV Report ,Virus classification ,Viral matrix protein ,biology ,DNA Viruses ,Virion ,ORDER THERMOPROTEALES ,Tristromaviridae ,biology.organism_classification ,030104 developmental biology ,chemistry ,Lytic cycle ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,DNA, Viral ,Taxonomy (biology) ,DNA ,Archaea - Abstract
International audience; Tristromaviridae is a family of viruses with linear, double-stranded DNA genomes of 16-18 kbp. The flexible, filamentous virions (400±20 nm×30±3 nm) consist of an envelope and an inner core constructed from two structural units: a rod-shaped helical nucleocapsid and a nucleocapsid-encompassing matrix protein layer. Tristromaviruses are lytic and infect hyperthermophilic archaea of the order Thermoproteales. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the Tristromaviridae, which is available at www.ictv.global/report/tristromaviridae.
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- 2018
34. Viruses of the <scp>A</scp> rchaea
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Tamara Basta, David Prangishvili, Roger A. Garrett, and Mart Krupovic
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0301 basic medicine ,Genetics ,viruses ,030106 microbiology ,DNA virus ,Archaeal Viruses ,Biology ,biology.organism_classification ,Genome ,Virology ,Virus ,03 medical and health sciences ,030104 developmental biology ,Viral replication ,Viral evolution ,Non-cellular life ,Archaea - Abstract
Double-stranded DNA (dsDNA) viruses infecting the Archaea form a unique group in viral world. They reveal exceptionally diverse, complex morphotypes, never encountered among dsDNA viruses of the Bacteria or Eukarya, and carry genomes with the overwhelming majority of genes without homologues in extant databases, other than in other archaeal viruses.
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- 2016
35. Analysis of metagenomic data reveals common features of halophilic viral communities across continents
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Jean-Christophe Auguet, Patrick Forterre, David Prangishvili, Viviane Ravet, Thierry Bouvier, Simon Roux, François Enault, Didier Debroas, Yvan Bettarel, Soizick Lucas-Staat, Télesphore Sime-Ngando, Jonathan Colombet, and Agnès Vellet
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0301 basic medicine ,Genetic diversity ,biology ,Ecology ,biology.organism_classification ,Microbiology ,Halophile ,03 medical and health sciences ,030104 developmental biology ,Caudovirales ,Metagenomics ,Genetic variation ,Clade ,Gene ,Ecology, Evolution, Behavior and Systematics ,Archaea - Abstract
Microbial communities from hypersaline ponds, dominated by halophilic archaea, are considered specific of such extreme conditions. The associated viral communities have accordingly been shown to display specific features, such as similar morphologies among different sites. However, little is known about the genetic diversity of these halophilic viral communities across the Earth. Here, we studied viral communities in hypersaline ponds sampled on the coast of Senegal (8-36% of salinity) using metagenomics approach, and compared them with hypersaline viromes from Australia and Spain. The specificity of hyperhalophilic viruses could first be demonstrated at a community scale, salinity being a strong discriminating factor between communities. For the major viral group detected in all samples (Caudovirales), only a limited number of halophilic Caudovirales clades were highlighted. These clades gather viruses from different continents and display consistent genetic composition, indicating that they represent related lineages with a worldwide distribution. Non-tailed hyperhalophilic viruses display a greater rate of gene transfer and recombination, with uncharacterized genes conserved across different kind of viruses and plasmids. Thus, hypersaline viral communities around the world appear to form a genetically consistent community that are likely to harbour new genes coding for enzymes specifically adapted to these environments.
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- 2015
36. A Novel Packing for A-Form DNA in an Icosahedral Virus
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Zhangli Su, Stefan Schouten, Ying Liu, David Prangishvili, Fengbin Wang, Mart Krupovic, Edward H. Egelman, and James F. Conway
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Crystallography ,Icosahedral symmetry ,Chemistry ,Biophysics ,A-DNA ,Virus - Published
- 2020
37. Centennial celebration of the bacteriophage research
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Patrick Forterre, Mart Krupovic, David Prangishvili, Mzia Kutateladze, Laurent Debarbieux, Département de Microbiologie - Department of Microbiology, Institut Pasteur [Paris], George Eliava Institute of Bacteriophages, Microbiology and Virology [Tbilisi, Georgia], and Institut Pasteur [Paris] (IP)
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0301 basic medicine ,MESH: Humans ,Biomedical Research ,MESH: Biomedical Research ,[SDV]Life Sciences [q-bio] ,030106 microbiology ,General Medicine ,Biology ,biology.organism_classification ,Microbiology ,[SDV.MP.BAC]Life Sciences [q-bio]/Microbiology and Parasitology/Bacteriology ,Bacteriophage ,[SHS.HISPHILSO]Humanities and Social Sciences/History, Philosophy and Sociology of Sciences ,stomatognathic diseases ,03 medical and health sciences ,030104 developmental biology ,Centennial ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,otorhinolaryngologic diseases ,Humans ,Bacteriophages ,MESH: Bacteriophages ,Molecular Biology ,Classics - Abstract
International audience; The year 2017 marked the 100th anniversary of the publication of Félix d’Herelle entitled “On an invisible microbe antagonistic toward dysenteric bacilli” in which he coined the term “bacteriophage [...]
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- 2018
38. Rolling-circle replication initiation protein of haloarchaeal sphaerolipovirus SNJ1 is homologous to bacterial transposases of the IS
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Yuchen, Wang, Beibei, Chen, Mengzhuo, Cao, Linshan, Sima, David, Prangishvili, Xiangdong, Chen, and Mart, Krupovic
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For most archaeal viruses, the mechanisms of genome replication are poorly understood, while the nature and provenance of their replication proteins are usually unknown. Here we show that replication of the circular double-stranded DNA genome of the halophilic
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- 2018
39. Viruses of archaea: Structural, functional, environmental and evolutionary genomics
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Virginija Cvirkaite-Krupovic, Mart Krupovic, David Prangishvili, Eugene V. Koonin, Jaime Iranzo, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], National Center for Biotechnology Information (NCBI), M.K. is supported by l'Agence Nationale de la Recherche (France) project ENVIRA. D.P. is supported by the European Union's Horizon 2020 research and innovation programme under grant agreement 685778, project VIRUS-X. J.I. and E.V.K. are supported by intramural funds of the US Department of Health and Human Services (to the National Library of Medicine)., ANR-17-CE15-0005,ENVIRA,Remodelage de la membrane cytoplasmique par les virus enveloppés d'archées(2017), European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016), and Institut Pasteur [Paris] (IP)
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Archaeal Viruses ,0301 basic medicine ,Aquatic Organisms ,Cancer Research ,MESH: Sequence Analysis, DNA ,Thaumarchaeota ,viruses ,[SDV]Life Sciences [q-bio] ,Genome ,MESH: Archaeal Viruses ,MESH: Genetic Variation ,MESH: Phylogeny ,Phylogeny ,MESH: Evolution, Molecular ,biology ,Ecology ,Infectious Diseases ,MESH: Archaea ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,MESH: Virion ,MESH: Metagenomics ,MESH: Genome, Viral ,Functional genomics ,MESH: Aquatic Organisms ,MESH: Interspersed Repetitive Sequences ,Genomics ,Genome, Viral ,Article ,Evolution, Molecular ,Viral Proteins ,03 medical and health sciences ,Virology ,[SDV.BBM.GTP]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Genomics [q-bio.GN] ,Human virome ,14. Life underwater ,Virion ,Genetic Variation ,Sequence Analysis, DNA ,biology.organism_classification ,Archaea ,MESH: Viral Proteins ,Interspersed Repetitive Sequences ,MESH: Microbial Interactions ,030104 developmental biology ,Evolutionary biology ,Metagenomics ,Microbial Interactions - Abstract
International audience; Viruses of archaea represent one of the most enigmatic parts of the virosphere. Most of the characterized archaeal viruses infect extremophilic hosts and display remarkable diversity of virion morphotypes, many of which have never been observed among viruses of bacteria or eukaryotes. The uniqueness of the virion morphologies is matched by the distinctiveness of the genomes of these viruses, with ∼75% of genes encoding unique proteins, refractory to functional annotation based on sequence analyses. In this review, we summarize the state-of-the-art knowledge on various aspects of archaeal virus genomics. First, we outline how structural and functional genomics efforts provided valuable insights into the functions of viral proteins and revealed intricate details of the archaeal virus-host interactions. We then highlight recent metagenomics studies, which provided a glimpse at the diversity of uncultivated viruses associated with the ubiquitous archaea in the oceans, including Thaumarchaeota, Marine Group II Euryarchaeota, and others. These findings, combined with the recent discovery that archaeal viruses mediate a rapid turnover of thaumarchaea in the deep sea ecosystems, illuminate the prominent role of these viruses in the biosphere. Finally, we discuss the origins and evolution of archaeal viruses and emphasize the evolutionary relationships between viruses and non-viral mobile genetic elements. Further exploration of the archaeal virus diversity as well as functional studies on diverse virus-host systems are bound to uncover novel, unexpected facets of the archaeal virome.
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- 2018
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40. Atomic Structure of Nearly Indestructible Pili from a Hyperthermophilic Acidophile
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Virginija Cvirkaite-Krupovic, Joe S. Wall, David Prangishvili, Edward H. Egelman, Fengbin Wang, and Mart Krupovic
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Chemistry ,Acidophile ,Biophysics ,Pilus - Published
- 2019
41. Ratification vote on taxonomic proposals to the International Committee on Taxonomy of Viruses (2015)
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Stuart G. Siddell, Eric B. Carstens, Andrew M. Q. King, Michael J. Adams, David Prangishvili, Elliot J. Lefkowitz, Said A. Ghabrial, Mya Breitbart, Peter J. Krell, Dennis H. Bamford, Rob Lavigne, Peter Simmonds, Hélène Sanfaçon, Andrew J. Davison, Alexander E. Gorbalenya, and Nick J. Knowles
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GeneralLiterature_INTRODUCTORYANDSURVEY ,viruses ,education ,ComputingMilieux_LEGALASPECTSOFCOMPUTING ,General Medicine ,Biology ,Virology ,Executive committee ,ComputingMilieux_MANAGEMENTOFCOMPUTINGANDINFORMATIONSYSTEMS ,Law ,Classification methods ,Taxonomy (biology) ,sense organs ,skin and connective tissue diseases ,Ratification ,Cherry necrotic rusty mottle virus ,GeneralLiterature_REFERENCE(e.g.,dictionaries,encyclopedias,glossaries) ,health care economics and organizations ,Virus classification - Abstract
Changes to virus taxonomy approved and ratified by the International Committee on Taxonomy of Viruses in February 2015 are listed. ispartof: Archives of Virology vol:160 issue:7 pages:1837-50 ispartof: location:Austria status: published
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- 2015
42. Archaeal viruses: living fossils of the ancient virosphere?
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David Prangishvili
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viruses ,General Neuroscience ,Archaeal Viruses ,Biology ,biology.organism_classification ,Virology ,General Biochemistry, Genetics and Molecular Biology ,Virus ,History and Philosophy of Science ,Phylogenetics ,Evolutionary biology ,Viral evolution ,Three-domain system ,Non-cellular life ,Living fossil ,Archaea - Abstract
Studies on viruses parasitizing archaea reveal their specific nature and complete the tripartite division of the biosphere, indicating that each of the three domains of life-Archaea, Bacteria, and Eukarya-has its own set of associated DNA viruses. I argue that the remarkable morphotypical diversity of archaea-specific viruses could have originated from diverse viral archetypes that predated the divergence of the three domains of cellular life. It is possible that the descendants of many of these viral archetypes are able to parasitize extant archaea owing to their ability to evade archaea-specific defenses against virus infection, specifically the defenses linked to the evolution of cell envelope structure.
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- 2015
43. DNA-Interacting Characteristics of the Archaeal Rudiviral Protein SIRV2_Gp1
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Clare Rollie, Eveline Peeters, M. Boon, Tessa E. F. Quax, Malcolm F. White, Rob Lavigne, Marleen Voet, David Prangishvili, Ronnie Willaert, Molecular Microbiology, BBSRC, University of St Andrews. School of Biology, University of St Andrews. Biomedical Sciences Research Complex, Department of Bio-engineering Sciences, Structural Biology Brussels, Microbiology, and Faculty of Sciences and Bioengineering Sciences
- Subjects
0301 basic medicine ,QH301 Biology ,lcsh:QR1-502 ,Rudiviridae ,Rudiviridae/genetics ,Genome ,SIRV2 ,lcsh:Microbiology ,chemistry.chemical_compound ,Sulfolobus/virology ,Virus Release ,helix-turn-helix domain ,Helix-turn-helix doman ,Host cell surface ,biology ,Viral Proteins/chemistry ,Archaeal Viruses ,Sulfolobus ,Cell biology ,DNA-Binding Proteins ,Infectious Diseases ,QR355 Virology ,DNA-Binding Proteins/chemistry ,Archaeal virus ,archaea ,Protein domain ,NDAS ,Genome, Viral ,Solfolobus ,Article ,Microbiology ,QH301 ,03 medical and health sciences ,Viral Proteins ,Protein Domains ,Virology ,DNA binding ,DNA/chemistry ,Gene ,QR355 ,Virion ,DNA ,archaeal virus ,biology.organism_classification ,Archaea ,030104 developmental biology ,chemistry ,Nucleic Acid Conformation - Abstract
Whereas the infection cycles of many bacterial and eukaryotic viruses have been characterized in detail, those of archaeal viruses remain largely unexplored. Recently, studies on a few model archaeal viruses such as SIRV2 (Sulfolobus islandicus rod-shaped virus) have revealed an unusual lysis mechanism that involves the formation of pyramidal egress structures on the host cell surface. To expand understanding of the infection cycle of SIRV2, we aimed to functionally characterize gp1, which is a SIRV2 gene with unknown function. The SIRV2_Gp1 protein is highly expressed during early stages of infection and it is the only protein that is encoded twice on the viral genome. It harbours a helix-turn-helix motif and was therefore hypothesized to bind DNA. The DNA-binding behavior of SIRV2_Gp1 was characterized with electrophoretic mobility shift assays and atomic force microscopy. We provide evidence that the protein interacts with DNA and that it forms large aggregates, thereby causing extreme condensation of the DNA. Furthermore, the N-terminal domain of the protein mediates toxicity to the viral host Sulfolobus. Our findings may lead to biotechnological applications, such as the development of a toxic peptide for the containment of pathogenic bacteria, and add to our understanding of the Rudiviral infection cycle. ispartof: VIRUSES-BASEL vol:9 issue:7 ispartof: location:Switzerland status: published
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- 2017
44. Author response: Model for a novel membrane envelope in a filamentous hyperthermophilic virus
- Author
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Mart Krupovic, Soizick Lucas-Staat, Frank DiMaio, Edward H. Egelman, David Prangishvili, Peter M. Kasson, Xiong Yu, and Stefan Schouten
- Subjects
Membrane ,Response model ,Chemistry ,Biophysics ,Virus ,Envelope (waves) - Published
- 2017
45. Model for a novel membrane envelope in a filamentous hyperthermophilic virus
- Author
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David Prangishvili, Xiong Yu, Soizick Lucas-Staat, Frank DiMaio, Stefan Schouten, Peter M. Kasson, Mart Krupovic, Edward H. Egelman, University of Virginia, University of Washington [Seattle], Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Royal Netherlands Institute for Sea Research (NIOZ), Utrecht University [Utrecht], This work was supported by NIH GM035269 (to EHE) and GM098304 (to PK), and by Agence Nationale de la Recherche grant ANR-13-BSV3-0017-01 (to DP) Computational resources were supported by Google., We thank Denise Dorhout (NIOZ) for analytical assistance., ANR-13-BSV3-0017,EXAVIR,Exit and assembly of hyperthermophilic archaeal viruses(2013), University of Virginia [Charlottesville], and Institut Pasteur [Paris]
- Subjects
0301 basic medicine ,QH301-705.5 ,archaea ,Science ,[SDV]Life Sciences [q-bio] ,030106 microbiology ,cryo-electron microscopy ,MESH: Membranes ,General Biochemistry, Genetics and Molecular Biology ,03 medical and health sciences ,biophysics ,structural biology ,Extreme environment ,Biology (General) ,Organism ,Membranes ,General Immunology and Microbiology ,biology ,General Neuroscience ,Bilayer ,Cryoelectron Microscopy ,DNA Viruses ,Membrane structure ,General Medicine ,Biophysics and Structural Biology ,biology.organism_classification ,MESH: DNA Viruses ,Cell biology ,030104 developmental biology ,Membrane ,Structural biology ,13. Climate action ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Medicine ,MESH: Acidianus ,MESH: Cryoelectron Microscopy ,Other ,Acidianus ,Research Article ,Archaea - Abstract
Biological membranes create compartments, and are usually formed by lipid bilayers. However, in hyperthermophilic archaea that live optimally at temperatures above 80°C the membranes are monolayers which resemble fused bilayers. Many double-stranded DNA viruses which parasitize such hosts, including the filamentous virus AFV1 of Acidianus hospitalis, are enveloped with a lipid-containing membrane. Using cryo-EM, we show that the membrane in AFV1 is a ~2 nm-thick monolayer, approximately half the expected membrane thickness, formed by host membrane-derived lipids which adopt a U-shaped ‘horseshoe’ conformation. We hypothesize that this unusual viral envelope structure results from the extreme curvature of the viral capsid, as ‘horseshoe’ lipid conformations favor such curvature and host membrane lipids that permit horseshoe conformations are selectively recruited into the viral envelope. The unusual envelope found in AFV1 also has many implications for biotechnology, since this membrane can survive the most aggressive conditions involving extremes of temperature and pH. DOI: http://dx.doi.org/10.7554/eLife.26268.001, eLife digest Virtually every environment on the planet is home to some form of life, even places that, at first glance, appear to be too harsh for any organism to survive in. For example, a microscopic organism known as Acidianus hospitalis thrives in highly acidic environments that are hotter than 80°C, conditions that would kill humans and many other species. Acidianus hospitalis has many adaptations that allow it to survive in its extreme environment. For example, the membrane that surrounds its cells has a different structure to the membranes that surround the cells of most other species. Membranes are made of molecules known as lipids. Generally these lipids assemble into two distinct layers (known as a bilayer) to form the membrane. However, in A. hospitalis the membrane contains only a single layer of lipids that resembles a bilayer in which lipids in opposite layers have fused together to make longer molecules. A virus known as AFV1 is able to infect A. hospitalis. Like many other viruses, AFV1 steals part of its host cell’s membrane when it leaves the cell in search of new cells to infect. This stolen membrane helps to protect the virus from its surroundings, however, the structure of the membrane surrounding AFV1 was not known. Kasson et al. combined a technique called cryo-electron microscopy with computer simulations to study the membrane surrounding AFV1. The study shows that this membrane is only half as thick as the membrane that surrounds A. hospitalis. To make this thinner membrane, flexible lipid molecules from the A. hospitalis membrane bend into a U-shape. These findings reveal a new type of membrane structure not previously seen in the natural world. In the future, this thinner membrane could have many uses in biotechnology, such as to make probes for medical imaging in patients or to deliver drugs to specific sites in the body. Enveloped by this unusual membrane, these structures may be more resistant to the normal processes that degrade and destroy foreign materials in humans and other organisms. DOI: http://dx.doi.org/10.7554/eLife.26268.002
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- 2017
46. A Novel Type of Polyhedral Viruses Infecting Hyperthermophilic Archaea
- Author
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David Prangishvili, Gérard Pehau-Arnaudet, Yoshizumi Ishino, Mart Krupovic, Ying Liu, Sonoko Ishino, Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris], Kyushu University [Fukuoka], Microscopie ultrastructurale - Ultrapole (CITECH), This work was supported by the European Union's Horizon 2020 research and innovation program under grant agreement 685778, project VIRUS-X., We are grateful to E. V. Koonin and T. G. Senkevich for their help in collecting environmental samples from hot springs in Beppu, Japan, to M. Duchateau (Proteomics Platform, Institut Pasteur) for help with proteomics analyses, and to M. Nilges and the Equipex CACSICE for providing the Falcon II direct detector., European Project: 685778,H2020,H2020-LEIT-BIO-2015-1,Virus-X(2016), Institut Pasteur [Paris] (IP), and Kyushu University
- Subjects
0301 basic medicine ,MESH: Sequence Analysis, DNA ,MESH: Sequence Homology, Amino Acid ,viruses ,[SDV]Life Sciences [q-bio] ,virion structure ,Genome ,hyperthermophile ,MESH: Gene Order ,Gene Order ,Genetics ,biology ,viral genome ,Archaeal Viruses ,MESH: DNA Viruses ,Sulfolobus ,Capsid ,MESH: Sulfolobus ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,MESH: Virion ,MESH: Genome, Viral ,archaea ,Immunology ,Genome, Viral ,MESH: Microscopy, Electron ,Microbiology ,Virus ,03 medical and health sciences ,Open Reading Frames ,Viral Proteins ,MESH: Viral Structures ,Virology ,[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology ,Viral Structures ,Sequence Homology, Amino Acid ,DNA Viruses ,Virion ,Sequence Analysis, DNA ,MESH: Open Reading Frames ,biology.organism_classification ,MESH: Viral Proteins ,Hyperthermophile ,Open reading frame ,Microscopy, Electron ,030104 developmental biology ,Genetic Diversity and Evolution ,Insect Science ,Archaea - Abstract
Encapsidation of genetic material into polyhedral particles is one of the most common structural solutions employed by viruses infecting hosts in all three domains of life. Here, we describe a new virus of hyperthermophilic archaea, Sulfolobus polyhedral virus 1 (SPV1), which condenses its circular double-stranded DNA genome in a manner not previously observed for other known viruses. The genome complexed with virion proteins is wound up sinusoidally into a spherical coil which is surrounded by an envelope and further encased by an outer polyhedral capsid apparently composed of the 20-kDa virion protein. Lipids selectively acquired from the pool of host lipids are integral constituents of the virion. None of the major virion proteins of SPV1 show similarity to structural proteins of known viruses. However, minor structural proteins, which are predicted to mediate host recognition, are shared with other hyperthermophilic archaeal viruses infecting members of the order Sulfolobales . The SPV1 genome consists of 20,222 bp and contains 45 open reading frames, only one-fifth of which could be functionally annotated. IMPORTANCE Viruses infecting hyperthermophilic archaea display a remarkable morphological diversity, often presenting architectural solutions not employed by known viruses of bacteria and eukaryotes. Here we present the isolation and characterization of Sulfolobus polyhedral virus 1, which condenses its genome into a unique spherical coil. Due to the original genomic and architectural features of SPV1, the virus should be considered a representative of a new viral family, “Portogloboviridae.”
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- 2017
47. Hard out there: understanding archaeal virus biology
- Author
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David Prangishvili, Emmanuelle R. J. Quemin, and Mart Krupovic
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Genetics ,Virology ,Viral evolution ,Biology ,biology.organism_classification ,Hyperthermophile ,Virus ,Archaea - Published
- 2014
48. Identification of the minimal replicon and the origin of replication of the crenarchaeal plasmid pRN1
- Author
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Silvia Berkner, Mery Pina Hinojosa, Georg Lipps, and David Prangishvili
- Subjects
DNA Replication ,Archaeal plasmid ,Archaeal Proteins ,Molecular Sequence Data ,pRN1 ,Replication Origin ,Biology ,Origin of replication ,Pre-replication complex ,Microbiology ,Sulfolobus ,Open Reading Frames ,Replication factor C ,Control of chromosome duplication ,Minichromosome maintenance ,Operon ,Replicon ,Original Research ,Genetics ,Sulfolobus acidocaldarius ,Base Sequence ,crenarchaea ,Inverted Repeat Sequences ,Ter protein ,origin of replication ,Nucleic Acid Conformation ,Origin recognition complex ,minimal replicon ,Plasmids - Abstract
We have determined the minimal replicon of the crenarchaeal plasmid pRN1. It consists of 3097 base pairs amounting to 58% of the genome of pRN1. The minimal replicon comprises replication operon orf56/orf904 coding for a transcriptional repressor and the replication protein of pRN1. An upstream region of 64 bp that contains the promoter of the replication operon is essential as well as 166 bp of sequence downstream of the orf904 gene. This region contains a putative transcriptional terminator and a 100 nucleotides long stem–loop structure. Only the latter structure was shown to be required for replication. In addition replication was sustained when the stem–loop was displaced to another part of the pRN1 sequence. By mutational analysis we also find that the integrity of the stem–loop structure is required to maintain the replication of pRN1-derived constructs. As similar stem–loop structures are also present in other members of the pRN family, we suggest that this conserved structural element could be the origin of replication for the pRN plasmids. Further bioinformatic analysis revealed that the domain structure of the replication protein and the presence of a similar stem–loop structure as the putative replication origin are also found in several bacteriophages.
- Published
- 2014
49. Protein-Protein Interactions Leading to Recruitment of the Host DNA Sliding Clamp by the Hyperthermophilic Sulfolobus islandicus Rod-Shaped Virus 2
- Author
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Malcolm F. White, Mart Krupovic, Andrew F. Gardner, David Prangishvili, Stephen D. Bell, New England Biolabs, Indiana University [Bloomington], Indiana University System, University of St Andrews [Scotland], Biologie Moléculaire du Gène chez les Extrêmophiles (BMGE), Institut Pasteur [Paris] (IP), Institut Pasteur [Paris], University of St Andrews. School of Biology, and University of St Andrews. Biomedical Sciences Research Complex
- Subjects
Models, Molecular ,QH301 Biology ,Archaeal Proteins ,[SDV]Life Sciences [q-bio] ,Molecular Sequence Data ,Immunology ,Eukaryotic DNA replication ,MESH: Amino Acid Sequence ,Biology ,Virus Replication ,Microbiology ,DNA polymerase delta ,Sulfolobus ,QH301 ,Viral Proteins ,Replication factor C ,SeqA protein domain ,Control of chromosome duplication ,Proliferating Cell Nuclear Antigen ,Virology ,MESH: Protein Binding ,Amino Acid Sequence ,Genetics ,MESH: Molecular Sequence Data ,DNA clamp ,MESH: DNA, Archaeal ,MESH: Virus Replication ,DNA replication ,MESH: Archaeal Proteins ,MESH: Viral Proteins ,Rudiviridae ,Genome Replication and Regulation of Viral Gene Expression ,3. Good health ,DNA, Archaeal ,MESH: Proliferating Cell Nuclear Antigen ,[SDV.MP]Life Sciences [q-bio]/Microbiology and Parasitology ,MESH: Sulfolobus ,Insect Science ,MESH: Rudiviridae ,[SDV.MP.VIR]Life Sciences [q-bio]/Microbiology and Parasitology/Virology ,Replisome ,MESH: Models, Molecular ,Protein Binding - Abstract
Viruses infecting hyperthermophilic archaea typically do not encode DNA polymerases, raising questions regarding their genome replication. Here, using a yeast two-hybrid approach, we have assessed interactions between proteins of Sulfolobus islandicus rod-shaped virus 2 (SIRV2) and the host-encoded proliferating cell nuclear antigen (PCNA), a key DNA replication protein in archaea. Five SIRV2 proteins were found to interact with PCNA, providing insights into the recruitment of host replisome for viral DNA replication.
- Published
- 2014
50. Unique genome replication mechanism of the archaeal virus AFV1
- Author
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Tamara Basta, Diego Cortez, Sarah Lambert, Tessa E. F. Quax, Sonia Baconnais, Alexandra Joubert, Stephen D. Bell, Eric Le Cam, Mery Pina, David Prangishvili, and Patrick Forterre
- Subjects
Genetics ,0303 health sciences ,Genome evolution ,030306 microbiology ,Biology ,Pre-replication complex ,Microbiology ,Genome ,03 medical and health sciences ,Viral replication ,Origin recognition complex ,Viral genome replication ,Molecular Biology ,Gene ,030304 developmental biology ,Genomic organization - Abstract
Summary The exceptional genomic content and genome organization of the Acidianus filamentous virus 1 (AFV1) that infects the hyperthermophilic archaeon Acidianus hospitalis suggest that this virus might exploit an unusual mechanism of genome replication. An analysis of replicative intermediates of the viral genome by two-dimensional (2D) agarose gel electrophoresis revealed that viral genome replication starts by the formation of a D-loop and proceeds via strand displacement replication. Characterization of replicative intermediates using dark-field electron microscopy, in combination with the 2D agarose gel electrophoresis data, suggests that recombination plays a key role in the termination of AFV1 genome replication through the formation of terminal loops. A terminal protein was found to be attached to the ends of the viral genome. The results allow us to postulate a model of genome replication that relies on recombination events for initiation and termination.
- Published
- 2014
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