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Mark J. Young - One of the best experts on this subject based on the ideXlab platform.

  • correction for hartman et al discovery and characterization of thermoproteus spherical piliferous Virus 1 a spherical Archaeal Virus decorated with unusual filaments
    Journal of Virology, 2020
    Co-Authors: Ross Hartman, Eric S. Boyd, Martin C Lawrence, Lieuwe Biewenga, Jacob Munsonmcgee, Mohammed Y Refai, Brian Bothner, Mark J. Young
    Abstract:

    Volume 94, no. 11, e00036-20, 2020, [https://doi.org/10.1128/JVI.00036-20][1]. Page 1, Abstract, line 10: “micrometers” should read “nanometers.” [1]: /lookup/doi/10.1128/JVI.00036-20

  • discovery and characterization of thermoproteus spherical piliferous Virus 1 a spherical Archaeal Virus decorated with unusual filaments
    Journal of Virology, 2020
    Co-Authors: Ross Hartman, Eric S. Boyd, Martin C Lawrence, Lieuwe Biewenga, Jacob Munsonmcgee, Mohammed Y Refai, Brian Bothner, Mark J. Young
    Abstract:

    We describe the discovery of an Archaeal Virus, one that infects archaea, tentatively named Thermoproteus spherical piliferous Virus 1 (TSPV1), which was purified from a Thermoproteales host isolated from a hot spring in Yellowstone National Park (USA). TSPV1 packages an 18.65-kb linear double-stranded DNA (dsDNA) genome with 31 open reading frames (ORFs), whose predicted gene products show little homology to proteins with known functions. A comparison of Virus particle morphologies and gene content demonstrates that TSPV1 is a new member of the Globuloviridae family of Archaeal Viruses. However, unlike other Globuloviridae members, TSPV1 has numerous highly unusual filaments decorating its surface, which can extend hundreds of nanometers from the virion. To our knowledge, similar filaments have not been observed in any other Archaeal Virus. The filaments are remarkably stable, remaining intact across a broad range of temperature and pH values, and they are resistant to chemical denaturation and proteolysis. A major component of the filaments is a glycosylated 35-kDa TSPV1 protein (TSPV1 GP24). The filament protein lacks detectable homology to structurally or functionally characterized proteins. We propose, given the low host cell densities of hot spring environments, that the TSPV1 filaments serve to increase the probability of Virus attachment and entry into host cells.IMPORTANCE High-temperature environments have proven to be an important source for the discovery of new Archaeal Viruses with unusual particle morphologies and gene content. Our isolation of Thermoproteus spherical piliferous Virus 1 (TSPV1), with numerous filaments extending from the virion surface, expands our understanding of viral diversity and provides new insight into viral replication in high-temperature environments.

  • survey of high resolution Archaeal Virus structures
    Current Opinion in Virology, 2019
    Co-Authors: Ross Hartman, Mark J. Young, Jacob Munsonmcgee, Charles Martin Lawrence
    Abstract:

    Archaeal Viruses exhibit diverse morphologies whose structures are just beginning to be explored at high-resolution. In this review, we update recent findings on Archaeal structural proteins and virion architectures and place them in the biological context in which these Viruses replicate. We conclude that many of the unusual structural features and dynamics of Archaeal Viruses aid their replication and survival in the chemically harsh environments, in which they replicate. Furthermore, we should expect to find more novel features from examining the high-resolution structures of additional Archaeal Viruses.

  • the molecular mechanism of cellular attachment for an Archaeal Virus
    Social Science Research Network, 2019
    Co-Authors: Ross Hartman, Mark J. Young, Jacob Munsonmcgee, Brian J Eilers, Daniel Bollschweiler, Harald Engelhardt, Charles Martin Lawrence
    Abstract:

    Sulfolobus turreted icosahedral Virus (STIV) is a model Archaeal Virus and member of the PRD1-AdenoVirus lineage. While it is known that STIV employs pyramidal lysis structures to exit the host, knowledge of the viral entry process is lacking. We therefore initiated studies on STIV attachment and entry. Negative stain and cryo-EM micrographs showed virion attachment to pili-like structures emanating from the Sulfolobus solfataricus host. Tomographic reconstruction and sub-tomogram averaging revealed pili recognition by the STIV C381 turret protein. Specifically, the triple jelly-roll structure of C381 determined by X-ray crystallography shows that pilus recognition is mediated by conserved surface residues in the 2nd and 3rd domains. Additionally, the STIV petal protein (C557), when present, occludes the pili binding site, suggesting it functions as a maturation protein. Combined, these results demonstrate a role for the namesake STIV turrets in initial cellular attachment and provide the first molecular model for viral attachment in the Archaeal domain of life.

  • Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods
    Journal of virology, 2016
    Co-Authors: Rebecca A. Hochstein, Eric S. Boyd, Maximiliano J. Amenabar, Jacob H. Munson-mcgee, Mark J. Young
    Abstract:

    ABSTRACT The field of viral metagenomics has expanded our understanding of viral diversity from all three domains of life (Archaea, Bacteria, and Eukarya). Traditionally, viral metagenomic studies provide information about viral gene content but rarely provide knowledge about virion morphology and/or cellular host identity. Here we describe a new Virus, Acidianus tailed spindle Virus (ATSV), initially identified by bioinformatic analysis of viral metagenomic data sets from a high-temperature (80°C) acidic (pH 2) hot spring located in Yellowstone National Park, followed by more detailed characterization using only environmental samples without dependency on culturing. Characterization included the identification of the large tailed spindle virion morphology, determination of the complete 70.8-kb circular double-stranded DNA (dsDNA) viral genome content, and identification of its cellular host. Annotation of the ATSV genome revealed a potential three-domain gene product containing an N-terminal leucine-rich repeat domain, followed by a likely posttranslation regulatory region consisting of high serine and threonine content, and a C-terminal ESCRT-III domain, suggesting interplay with the host ESCRT system. The host of ATSV, which is most closely related to Acidianus hospitalis, was determined by a combination of analysis of cellular clustered regularly interspaced short palindromic repeat (CRISPR)/Cas loci and dual viral and cellular fluorescence in situ hybridization (viral FISH) analysis of environmental samples and confirmed by culture-based infection studies. This work provides an expanded pathway for the discovery, isolation, and characterization of new Viruses using culture-independent approaches and provides a platform for predicting and confirming Virus hosts. IMPORTANCE Virus discovery and characterization have been traditionally accomplished by using culture-based methods. While a valuable approach, it is limited by the availability of culturable hosts. In this research, we report a Virus-centered approach to Virus discovery and characterization, linking viral metagenomic sequences to a Virus particle, its sequenced genome, and its host directly in environmental samples, without using culture-dependent methods. This approach provides a pathway for the discovery, isolation, and characterization of new Viruses. While this study used an acidic hot spring environment to characterize a new Archaeal Virus, Acidianus tailed spindle Virus (ATSV), the approach can be generally applied to any environment to expand knowledge of Virus diversity in all three domains of life.

David Prangishvili - One of the best experts on this subject based on the ideXlab platform.

  • a filamentous Archaeal Virus is enveloped inside the cell and released through pyramidal portals
    Proceedings of the National Academy of Sciences of the United States of America, 2021
    Co-Authors: David Prangishvili, Junfeng Liu, Diana P Baquero, Anastasia D Gazi, Martin Sachse, Christine Schmitt, Maryse Moyanilges, Stefan Schouten
    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-long Sulfolobus 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.

  • new Virus isolates from italian hydrothermal environments underscore the biogeographic pattern in Archaeal Virus communities
    bioRxiv, 2020
    Co-Authors: Diana P Baquero, David Prangishvili, Patrizia Contursi, Monica Piochi, Simonetta Bartolucci, Ying Liu, Virginija Cvirkaitekrupovic, M Krupovic
    Abstract:

    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 families Rudiviridae, Globuloviridae and Tristromaviridae were isolated and characterized. Two of these Viruses infect neutrophilic hyperthermophiles of the genus Pyrobaculum, whereas the remaining three have rod-shaped virions typical of the family Rudiviridae and infect acidophilic hyperthermophiles belonging to three different genera of the order Sulfolobales, namely, Saccharolobus, Acidianus and Metallosphaera. Notably, Metallosphaera rod-shaped Virus 1 is the first rudiVirus isolated on Metallosphaera species. 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 the Rudiviridae family, 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.

  • New Virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in Archaeal Virus communities
    ISME Journal, 2020
    Co-Authors: Diana Baquero, David Prangishvili, Patrizia Contursi, Monica Piochi, Simonetta Bartolucci, Ying Liu, Virginija Cvirkaite-krupovic, M Krupovic
    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 families Rudiviridae, Globuloviridae and Tristromaviridae were isolated and characterized. Two of these Viruses infect neutrophilic hyperthermophiles of the genus Pyrobaculum, whereas the remaining three have rod-shaped virions typical of the family Rudiviridae and infect acidophilic hyperthermophiles belonging to three different genera of the order Sulfolobales, namely, Saccharolobus, Acidianus, and Metallosphaera. Notably, Metallosphaera rod-shaped Virus 1 is the first rudiVirus isolated on Metallosphaera species. 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. Analysis of the CRISPR spacers suggests that isolated rudiViruses have experienced recent host switching across the genus boundary, potentially to escape the targeting by CRISPR-Cas immunity systems. Finally, we propose a revised classification of the Rudiviridae family, with the establishment of six 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.

  • Novel haloArchaeal Viruses from Lake Retba infecting Haloferax and Halorubrum species.
    Environmental Microbiology, 2019
    Co-Authors: Carolina Megumi Mizuno, David Prangishvili, Dennis H. Bamford, M Krupovic, Soizick Lucas-staat, Bina Prajapati, Télesphore Sime-ngando, Patrik Forterre, Hanna M. Oksanen
    Abstract:

    : 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.

  • Viruses of archaea structural functional environmental and evolutionary genomics
    Virus Research, 2018
    Co-Authors: M Krupovic, Virginija Cvirkaitekrupovic, Jaime Iranzo, David Prangishvili
    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 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.

Dennis H. Bamford - One of the best experts on this subject based on the ideXlab platform.

  • Novel haloArchaeal Viruses from Lake Retba infecting Haloferax and Halorubrum species.
    Environmental Microbiology, 2019
    Co-Authors: Carolina Megumi Mizuno, David Prangishvili, Dennis H. Bamford, M Krupovic, Soizick Lucas-staat, Bina Prajapati, Télesphore Sime-ngando, Patrik Forterre, Hanna M. Oksanen
    Abstract:

    : 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.

  • extremely halophilic pleomorphic Archaeal Virus hrpv9 extends the diversity of pleolipoViruses with integrases
    Research in Microbiology, 2018
    Co-Authors: Nina S Atanasova, Hanna M. Oksanen, Tatiana A Demina, Sudar Krishnam Rajan N V Shanthi, Dennis H. Bamford
    Abstract:

    Certain pleomorphic Archaeal Viruses are highly infectious even at saturated salt. These Viruses belong to the genus BetapleolipoVirus of the recently described Archaeal Virus family Pleolipoviridae. PleolipoViruses comprise single-stranded or double-stranded, circular or linear DNA genomes that share countless homologues among various Archaeal genetic elements. Here we describe a new extremely halophilic betapleolipoVirus, Halorubrum pleomorphic Virus 9 (HRPV9), which has an integrase gene. We also identified new genes encoding minor pleolipoviral structural proteins. The studies on HRPV9 enhance our knowledge on pleolipoViruses, especially their reciprocal relatedness and relation to certain Archaeal plasmids, proViruses and membrane vesicles.

  • lemon shaped halo Archaeal Virus his1 with uniform tail but variable capsid structure
    Proceedings of the National Academy of Sciences of the United States of America, 2015
    Co-Authors: Chuan Hong, Maija K. Pietilä, Dennis H. Bamford, Caroline J Fu, Michael F Schmid, Wah Chiu
    Abstract:

    Lemon-shaped Viruses are common in nature but so far have been observed to infect only archaea. Due to their unusual shape, the structures of these Viruses are challenging to study and therefore poorly characterized. Here, we have studied haloArchaeal Virus His1 using cryo-electron tomography as well as biochemical dissociation. The virions have different sizes, but prove to be extremely stable under various biochemical treatments. Subtomogram averaging of the computationally extracted virions resolved a tail-like structure with a central tail hub density and six tail spikes. Inside the tail there are two cavities and a plug density that separates the tail hub from the interior genome. His1 most likely uses the tail spikes to anchor to host cells and the tail hub to eject the genome, analogous to classic tailed bacteriophages. Upon biochemical treatment that releases the genome, the lemon-shaped virion transforms into an empty tube. Such a dramatic transformation demonstrates that the capsid proteins are capable of undergoing substantial quaternary structural changes, which may occur at different stages of the Virus life cycle.

  • DNA ejection from an Archaeal Virus--a single-molecule approach.
    Biophysical journal, 2013
    Co-Authors: Kalle Hanhijärvi, Maija K. Pietilä, Gabija Ziedaite, Edward Hæggström, Dennis H. Bamford
    Abstract:

    Abstract The translocation of genetic material from the viral capsid to the cell is an essential part of the viral infection process. Whether the energetics of this process is driven by the energy stored within the confined nucleic acid or cellular processes pull the genome into the cell has been the subject of discussion. However, in vitro studies of genome ejection have been limited to a few head-tailed bacteriophages with a double-stranded DNA genome. Here we describe a DNA release system that operates in an Archaeal Virus. This Virus infects an archaeon Haloarcula hispanica that was isolated from a hypersaline environment. The DNA-ejection velocity of His1, determined by single-molecule experiments, is comparable to that of bacterial Viruses. We found that the ejection process is modulated by the external osmotic pressure (polyethylene glycol (PEG)) and by increased ion (Mg 2+ and Na + ) concentration. The observed ejection was unidirectional, randomly paused, and incomplete, which suggests that cellular processes are required to complete the DNA transfer.

  • temperate membrane containing halophilic Archaeal Virus snj1 has a circular dsdna genome identical to that of plasmid phh205
    Virology, 2012
    Co-Authors: Ziqian Zhang, Dennis H. Bamford, Ying Liu, Shuai Wang, Di Yang, Yichen Cheng, Jin Chen, Yunjun Mei, Ping Shen, Xiangdong Chen
    Abstract:

    Abstract A temperate haloArchaeal Virus, SNJ1, was induced from the lysogenic host, Natrinema sp. J7-1, with mitomycin C, and the Virus produced plaques on lawns of Natrinema sp. J7-2. Optimization of the induction conditions allowed us to increase the titer from ∼10 4  PFU/ml to ∼10 11  PFU/ml. Single-step growth curves exhibited a burst size of ∼100 PFU/cell. The genome of SNJ1 was observed to be a circular, double-stranded DNA (dsDNA) molecule (16,341 bp). Surprisingly, the sequence of SNJ1 was identical to that of a previously described plasmid, pHH205, indicating that this plasmid is the proVirus of SNJ1. Several structural protein-encoding genes were identified in the viral genome. In addition, the comparison of putative packaging ATPase sequences from bacterial, Archaeal and eukaryotic Viruses, as well as the presence of lipid constituents from the host phospholipid pool, strongly suggest that SNJ1 belongs to the PRD1-type lineage of dsDNA Viruses, which have an internal membrane.

M Krupovic - One of the best experts on this subject based on the ideXlab platform.

  • Virus-induced cell gigantism and asymmetric cell division in archaea
    Proceedings of the National Academy of Sciences of the United States of America, 2021
    Co-Authors: Junfeng Liu, Diana Baquero, Virginija Cvirkaite-krupovic, Yunfeng Yang, Qi Zhang, Yulong Shen, M Krupovic
    Abstract:

    Archaeal Viruses represent one of the most mysterious parts of the global virosphere, with many Virus groups sharing no evolutionary relationship to Viruses of bacteria or eukaryotes. How these Viruses interact with their hosts remains largely unexplored. Here we show that nonlytic lemon-shaped Virus STSV2 interferes with the cell cycle control of its host, hyperthermophilic and acidophilic archaeon Sulfolobus islandicus, arresting the cell cycle in the S phase. STSV2 infection leads to transcriptional repression of the cell division machinery, which is homologous to the eukaryotic endosomal sorting complexes required for transport (ESCRT) system. The infected cells grow up to 20-fold larger in size, have 8,000-fold larger volume compared to noninfected cells, and accumulate massive amounts of viral and cellular DNA. Whereas noninfected Sulfolobus cells divide symmetrically by binary fission, the STSV2-infected cells undergo asymmetric division, whereby giant cells release normal-sized cells by budding, resembling the division of budding yeast. Reinfection of the normal-sized cells produces a new generation of giant cells. If the CRISPR-Cas system is present, the giant cells acquire Virus-derived spacers and terminate the Virus spread, whereas in its absence, the cycle continues, suggesting that CRISPR-Cas is the primary defense system in Sulfolobus against STSV2. Collectively, our results show how an Archaeal Virus manipulates the cell cycle, transforming the cell into a giant virion-producing factory.

  • new Virus isolates from italian hydrothermal environments underscore the biogeographic pattern in Archaeal Virus communities
    bioRxiv, 2020
    Co-Authors: Diana P Baquero, David Prangishvili, Patrizia Contursi, Monica Piochi, Simonetta Bartolucci, Ying Liu, Virginija Cvirkaitekrupovic, M Krupovic
    Abstract:

    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 families Rudiviridae, Globuloviridae and Tristromaviridae were isolated and characterized. Two of these Viruses infect neutrophilic hyperthermophiles of the genus Pyrobaculum, whereas the remaining three have rod-shaped virions typical of the family Rudiviridae and infect acidophilic hyperthermophiles belonging to three different genera of the order Sulfolobales, namely, Saccharolobus, Acidianus and Metallosphaera. Notably, Metallosphaera rod-shaped Virus 1 is the first rudiVirus isolated on Metallosphaera species. 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 the Rudiviridae family, 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.

  • New Virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in Archaeal Virus communities
    ISME Journal, 2020
    Co-Authors: Diana Baquero, David Prangishvili, Patrizia Contursi, Monica Piochi, Simonetta Bartolucci, Ying Liu, Virginija Cvirkaite-krupovic, M Krupovic
    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 families Rudiviridae, Globuloviridae and Tristromaviridae were isolated and characterized. Two of these Viruses infect neutrophilic hyperthermophiles of the genus Pyrobaculum, whereas the remaining three have rod-shaped virions typical of the family Rudiviridae and infect acidophilic hyperthermophiles belonging to three different genera of the order Sulfolobales, namely, Saccharolobus, Acidianus, and Metallosphaera. Notably, Metallosphaera rod-shaped Virus 1 is the first rudiVirus isolated on Metallosphaera species. 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. Analysis of the CRISPR spacers suggests that isolated rudiViruses have experienced recent host switching across the genus boundary, potentially to escape the targeting by CRISPR-Cas immunity systems. Finally, we propose a revised classification of the Rudiviridae family, with the establishment of six 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.

  • Novel haloArchaeal Viruses from Lake Retba infecting Haloferax and Halorubrum species.
    Environmental Microbiology, 2019
    Co-Authors: Carolina Megumi Mizuno, David Prangishvili, Dennis H. Bamford, M Krupovic, Soizick Lucas-staat, Bina Prajapati, Télesphore Sime-ngando, Patrik Forterre, Hanna M. Oksanen
    Abstract:

    : 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.

  • Viruses of archaea structural functional environmental and evolutionary genomics
    Virus Research, 2018
    Co-Authors: M Krupovic, Virginija Cvirkaitekrupovic, Jaime Iranzo, David Prangishvili
    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 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.

Martin C Lawrence - One of the best experts on this subject based on the ideXlab platform.

  • correction for hartman et al discovery and characterization of thermoproteus spherical piliferous Virus 1 a spherical Archaeal Virus decorated with unusual filaments
    Journal of Virology, 2020
    Co-Authors: Ross Hartman, Eric S. Boyd, Martin C Lawrence, Lieuwe Biewenga, Jacob Munsonmcgee, Mohammed Y Refai, Brian Bothner, Mark J. Young
    Abstract:

    Volume 94, no. 11, e00036-20, 2020, [https://doi.org/10.1128/JVI.00036-20][1]. Page 1, Abstract, line 10: “micrometers” should read “nanometers.” [1]: /lookup/doi/10.1128/JVI.00036-20

  • discovery and characterization of thermoproteus spherical piliferous Virus 1 a spherical Archaeal Virus decorated with unusual filaments
    Journal of Virology, 2020
    Co-Authors: Ross Hartman, Eric S. Boyd, Martin C Lawrence, Lieuwe Biewenga, Jacob Munsonmcgee, Mohammed Y Refai, Brian Bothner, Mark J. Young
    Abstract:

    We describe the discovery of an Archaeal Virus, one that infects archaea, tentatively named Thermoproteus spherical piliferous Virus 1 (TSPV1), which was purified from a Thermoproteales host isolated from a hot spring in Yellowstone National Park (USA). TSPV1 packages an 18.65-kb linear double-stranded DNA (dsDNA) genome with 31 open reading frames (ORFs), whose predicted gene products show little homology to proteins with known functions. A comparison of Virus particle morphologies and gene content demonstrates that TSPV1 is a new member of the Globuloviridae family of Archaeal Viruses. However, unlike other Globuloviridae members, TSPV1 has numerous highly unusual filaments decorating its surface, which can extend hundreds of nanometers from the virion. To our knowledge, similar filaments have not been observed in any other Archaeal Virus. The filaments are remarkably stable, remaining intact across a broad range of temperature and pH values, and they are resistant to chemical denaturation and proteolysis. A major component of the filaments is a glycosylated 35-kDa TSPV1 protein (TSPV1 GP24). The filament protein lacks detectable homology to structurally or functionally characterized proteins. We propose, given the low host cell densities of hot spring environments, that the TSPV1 filaments serve to increase the probability of Virus attachment and entry into host cells.IMPORTANCE High-temperature environments have proven to be an important source for the discovery of new Archaeal Viruses with unusual particle morphologies and gene content. Our isolation of Thermoproteus spherical piliferous Virus 1 (TSPV1), with numerous filaments extending from the virion surface, expands our understanding of viral diversity and provides new insight into viral replication in high-temperature environments.

  • isolation and characterization of metallosphaera turreted icosahedral Virus a founding member of a new family of Archaeal Viruses
    Journal of Virology, 2017
    Co-Authors: Cassia Wagner, Vijay S Reddy, Francisco J Asturias, Maryam Khoshouei, John E Johnson, Pilar Manrique, Jacob H Munsonmcgee, Wolfgang Baumeister, Martin C Lawrence
    Abstract:

    Our understanding of Archaeal Virus diversity and structure is just beginning to emerge. Here we describe a new Archaeal Virus, tentatively named Metallosphaera turreted icosahedral Virus (MTIV), that was isolated from an acidic hot spring in Yellowstone National Park, USA. Two strains of the Virus were identified and were found to replicate in an Archaeal host species closely related to Metallosphaera yellowstonensis Each strain encodes a 9.8- to 9.9-kb linear double-stranded DNA (dsDNA) genome with large inverted terminal repeats. Each genome encodes 21 open reading frames (ORFs). The ORFs display high homology between the strains, but they are quite distinct from other known viral genes. The 70-nm-diameter virion is built on a T=28 icosahedral lattice. Both single particle cryo-electron microscopy and cryotomography reconstructions reveal an unusual structure that has 42 turret-like projections: 12 pentameric turrets positioned on the icosahedral 5-fold axes and 30 turrets with apparent hexameric symmetry positioned on the icosahedral 2-fold axes. Both the virion structural properties and the genome content support MTIV as the founding member of a new family of Archaeal Viruses.IMPORTANCE Many Archaeal Viruses are quite different from Viruses infecting bacteria and eukaryotes. Initial characterization of MTIV reveals a Virus distinct from other known bacterial, eukaryotic, and Archaeal Viruses; this finding suggests that Viruses infecting Archaea are still an understudied group. As the first known Virus infecting a Metallosphaera sp., MTIV provides a new system for exploring Archaeal virology by examining host-Virus interactions and the unique features of MTIV structure-function relationships. These studies will likely expand our understanding of Virus ecology and evolution.

  • structural studies of e73 from a hyperthermophilic Archaeal Virus identify the rh3 domain an elaborated ribbon helix helix motif involved in dna recognition
    Biochemistry, 2012
    Co-Authors: Casey Schlenker, Martin C Lawrence, Mark J. Young, Anupam Goel, Brian P Tripet, Smita K Menon, Taylor Willi, Mensur Dlakic, Valerie Copie
    Abstract:

    Hyperthermophilic Archaeal Viruses, including Sulfolobus spindle-shaped Viruses (SSVs) such as SSV-1 and SSV-Ragged Hills, exhibit remarkable morphology and genetic diversity. However, they remain poorly understood, in part because their genomes exhibit limited or unrecognizable sequence similarity to genes with known function. Here we report structural and functional studies of E73, a 73-residue homodimeric protein encoded within the SSV-Ragged Hills genome. Despite lacking significant sequence similarity, the nuclear magnetic resonance (NMR) structure reveals clear similarity to ribbon–helix–helix (RHH) domains present in numerous proteins involved in transcriptional regulation. In vitro double-stranded DNA (dsDNA) binding experiments confirm the ability of E73 to bind dsDNA in a nonspecific manner with micromolar affinity, and characterization of the K11E variant confirms the location of the predicted DNA binding surface. E73 is distinct, however, from known RHH domains. The RHH motif is elaborated upo...

  • structure of an Archaeal Virus capsid protein reveals a common ancestry to eukaryotic and bacterial Viruses
    Proceedings of the National Academy of Sciences of the United States of America, 2005
    Co-Authors: Reza Khayat, Martin C Lawrence, Mark J. Young, Liang Tang, Eric T Larson, John E Johnson
    Abstract:

    Archaea and their Viruses are poorly understood when compared with the Eukarya and Bacteria domains of life. We report here the crystal structure of the major capsid protein (MCP) of the Sulfolobus turreted icosahedral Virus, an Archaeal Virus isolated from an acidic hot spring (pH 2–4, 72–92°C) in Yellowstone National Park. The structure is nearly identical to the MCP structures of the eukaryotic Paramecium bursaria Chlorella Virus, and the bacteriophage PRD1, and shows a common fold with the mammalian adenoVirus. Structural analysis of the capsid architecture, determined by fitting the subunit into the electron cryomicroscopy reconstruction of the Virus, identified a number of key interactions that are akin to those observed in adenoVirus and PRD1. The similar capsid proteins and capsid architectures strongly suggest that these viral capsids originated and evolved from a common ancestor. Hence, this work provides a previously undescribed example of a viral relationship spanning the three domains of life (Eukarya, Bacteria, and Archaea). The MCP structure also provides insights into the stabilizing forces required for extracellular hyperthermophilic proteins to tolerate high-temperature hot springs.