scholarly journals Isolation and Characterization of Metallosphaera Turreted Icosahedral Virus, a Founding Member of a New Family of Archaeal Viruses

2017 ◽  
Vol 91 (20) ◽  
Author(s):  
Cassia Wagner ◽  
Vijay Reddy ◽  
Francisco Asturias ◽  
Maryam Khoshouei ◽  
John E. Johnson ◽  
...  
Keyword(s):  
Hot Spring ◽  
Archaeal Virus ◽  
Content Type ◽  
Founding Member ◽  
New Family ◽  
Isolation And Characterization ◽  
Virus Diversity ◽  
Archaeal Viruses ◽  
Icosahedral Virus

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.

scholarly journals Acidianus Tailed Spindle Virus: a New Archaeal Large Tailed Spindle Virus Discovered by Culture-Independent Methods

2016 ◽  
Vol 90 (7) ◽  
pp. 3458-3468 ◽  
Author(s):  
Rebecca A. Hochstein ◽  
Maximiliano J. Amenabar ◽  
Jacob H. Munson-McGee ◽  
Eric S. Boyd ◽  
Mark J. Young
Keyword(s):  
Environmental Samples ◽  
Hot Spring ◽  
Metagenomic Data ◽  
Virus Discovery ◽  
Content Type ◽  
Isolation And Characterization ◽  
Virus Diversity ◽  
Culture Independent ◽  
Domains Of Life

ABSTRACTThe field of viral metagenomics has expanded our understanding of viral diversity from all three domains of life (Archaea,Bacteria, andEukarya). 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,Acidianustailed 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 toAcidianus hospitalis, was determined by a combination of analysis of cellular clustered regularly interspaced short palindromic repeat (CRISPR)/Cas loci and dual viral and cellular fluorescencein situhybridization (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.IMPORTANCEVirus 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,Acidianustailed spindle virus (ATSV), the approach can be generally applied to any environment to expand knowledge of virus diversity in all three domains of life.

scholarly journals Familial Relationships in Hyperthermo- and Acidophilic Archaeal Viruses

2010 ◽  
Vol 84 (9) ◽  
pp. 4747-4754 ◽  
Author(s):  
Lotta Johanna Happonen ◽  
Peter Redder ◽  
Xu Peng ◽  
Laila Johanne Reigstad ◽  
David Prangishvili ◽  
...  
Keyword(s):  
Structural Organization ◽  
Hot Springs ◽  
Three Dimensional ◽  
Life Cycles ◽  
Dimensional Structure ◽  
Archaeal Virus ◽  
Archaeal Viruses ◽  
Icosahedral Virus ◽  
Host Cell Interactions

ABSTRACT Archaea often live in extreme, harsh environments such as acidic hot springs and hypersaline waters. To date, only two icosahedrally symmetric, membrane-containing archaeal viruses, SH1 and Sulfolobus turreted icosahedral virus (STIV), have been described in detail. We report the sequence and three-dimensional structure of a third such virus isolated from a hyperthermoacidophilic crenarchaeon, Sulfolobus strain G4ST-2. Characterization of this new isolate revealed it to be similar to STIV on the levels of genome and structural organization. The genome organization indicates that these two viruses have diverged from a common ancestor. Interestingly, the prominent surface turrets of the two viruses are strikingly different. By sequencing and mass spectrometry, we mapped several large insertions and deletions in the known structural proteins that could account for these differences and showed that both viruses can infect the same host. A combination of genomic and proteomic analyses revealed important new insights into the structural organization of these viruses and added to our limited knowledge of archaeal virus life cycles and host-cell interactions.

scholarly journals Isolation and characterization of a thermophilic sulfur- and iron-reducing thaumarchaeote from a terrestrial acidic hot spring

2019 ◽  
Vol 13 (10) ◽  
pp. 2465-2474 ◽  
Author(s):  
Shingo Kato ◽  
Takashi Itoh ◽  
Masahiro Yuki ◽  
Mai Nagamori ◽  
Masafumi Ohnishi ◽  
...  
Keyword(s):  
Hot Spring ◽  
Isolation And Characterization

scholarly journals Isolation and Characterization of Akhmeta Virus from Wild-Caught Rodents (Apodemus spp.) in Georgia

2019 ◽  
Vol 93 (24) ◽  
Author(s):  
Jeffrey B. Doty ◽  
Giorgi Maghlakelidze ◽  
Irakli Sikharulidze ◽  
Shin-Lin Tu ◽  
Clint N. Morgan ◽  
...  
Keyword(s):  
Natural History ◽  
Molecular Characterization ◽  
Small Mammals ◽  
Skin Lesions ◽  
Human Populations ◽  
Content Type ◽  
Subsequent Investigation ◽  
Isolation And Characterization ◽  
History Of

ABSTRACT In 2013, a novel orthopoxvirus was detected in skin lesions of two cattle herders from the Kakheti region of Georgia (country); this virus was named Akhmeta virus. Subsequent investigation of these cases revealed that small mammals in the area had serological evidence of orthopoxvirus infections, suggesting their involvement in the maintenance of these viruses in nature. In October 2015, we began a longitudinal study assessing the natural history of orthopoxviruses in Georgia. As part of this effort, we trapped small mammals near Akhmeta (n = 176) and Gudauri (n = 110). Here, we describe the isolation and molecular characterization of Akhmeta virus from lesion material and pooled heart and lung samples collected from five wood mice (Apodemus uralensis and Apodemus flavicollis) in these two locations. The genomes of Akhmeta virus obtained from rodents group into 2 clades: one clade represented by viruses isolated from A. uralensis samples, and one clade represented by viruses isolated from A. flavicollis samples. These genomes also display several presumptive recombination events for which gene truncation and identity have been examined. IMPORTANCE Akhmeta virus is a unique Orthopoxvirus that was described in 2013 from the country of Georgia. This paper presents the first isolation of this virus from small mammal (Rodentia; Apodemus spp.) samples and the molecular characterization of those isolates. The identification of the virus in small mammals is an essential component to understanding the natural history of this virus and its transmission to human populations and could guide public health interventions in Georgia. Akhmeta virus genomes harbor evidence suggestive of recombination with a variety of other orthopoxviruses; this has implications for the evolution of orthopoxviruses, their ability to infect mammalian hosts, and their ability to adapt to novel host species.

scholarly journals In Vitro Isolation and Characterization of Oxazolidinone-Resistant Mycobacterium tuberculosis

2017 ◽  
Vol 61 (10) ◽  
Author(s):  
Matthew B. McNeil ◽  
Devon D. Dennison ◽  
Catherine D. Shelton ◽  
Tanya Parish
Keyword(s):  
Mycobacterium Tuberculosis ◽  
23S Rrna ◽  
Clinical Settings ◽  
Content Type ◽  
Isolation And Characterization ◽  
Mutant Strains ◽  
Ribosomal Protein L3 ◽  
Resistant Strains

ABSTRACT Oxazolidinones are promising candidates for the treatment of Mycobacterium tuberculosis infections. We isolated linezolid-resistant strains from H37Rv (Euro-American) and HN878 (East-Asian) strains; resistance frequencies were similar in the two strains. Mutations were identified in ribosomal protein L3 (RplC) and the 23S rRNA (rrl). All mutant strains were cross resistant to sutezolid; a subset was cross resistant to chloramphenicol. Mutations in rrl led to growth impairment and decreased fitness that may limit spread in clinical settings.

scholarly journals Isolation and Characterization of Thermophilic Bacteria from Zharkent geothermal hot spring

2019 ◽  
Vol 58 (1) ◽  
Author(s):  
A.S. Mashzhan ◽  
B. Nils-Kåre ◽  
A.S. Kistaubaeva ◽  
A.B. Talipova ◽  
Zh.K. Batykova ◽  
...  
Keyword(s):  
Hot Spring ◽  
Thermophilic Bacteria ◽  
Isolation And Characterization

scholarly journals Discovery and Characterization of Thermoproteus Spherical Piliferous Virus 1: a Spherical Archaeal Virus Decorated with Unusual Filaments

2020 ◽  
Vol 94 (11) ◽  
Author(s):  
Ross Hartman ◽  
Lieuwe Biewenga ◽  
Jacob Munson-McGee ◽  
Mohammed Refai ◽  
Eric S. Boyd ◽  
...  
Keyword(s):  
High Temperature ◽  
Hot Spring ◽  
Open Reading Frames ◽  
Host Cells ◽  
Gene Content ◽  
Archaeal Virus ◽  
Virus Attachment ◽  
Archaeal Viruses ◽  
Cell Densities ◽  
Filament Protein

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 micrometers 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.

scholarly journals Whole-Genome Sequences of Salmonella enterica subsp. enterica Serovar Typhimurium Strains TT6675 and TT9097 Employed in the Isolation and Characterization of a Giant Phage Mutant Collection

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Han Ming Gan ◽  
Wilhelm Wei Han Eng ◽  
Melissa K. Barton ◽  
Lily E. Adams ◽  
Nurul Aisyah Samsudin ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Phage Mutant ◽  
Isolation And Characterization ◽  
Serovar Typhimurium ◽  
Bacterial Viruses ◽  
Mutant Collection

ABSTRACT We report here the genome sequences of Salmonella enterica subsp. enterica serovar Typhimurium strains TT6675 and TT9097, which we utilize for genetic analyses of giant bacterial viruses. Our analyses identified several genetic variations between the two strains, most significantly confirming strain TT6675 as a serine suppressor and TT9097 as a nonsuppressor.

scholarly journals NovelSulfolobusVirus with an Exceptional Capsid Architecture

2017 ◽  
Vol 92 (5) ◽  
Author(s):  
Haina Wang ◽  
Zhenqian Guo ◽  
Hongli Feng ◽  
Yufei Chen ◽  
Xiuqiang Chen ◽  
...  
Keyword(s):  
Costa Rica ◽  
Host Cell ◽  
Lipid Membrane ◽  
Hot Spring ◽  
Longitudinal Axis ◽  
Viral Envelope ◽  
Open Reading Frames ◽  
Progeny Virus ◽  
Archaeal Virus ◽  
Content Type

ABSTRACTA novel archaeal virus, denotedSulfolobus ellipsoid virus 1(SEV1), was isolated from an acidic hot spring in Costa Rica. The morphologically unique virion of SEV1 contains a protein capsid with 16 regularly spaced striations and an 11-nm-thick envelope. The capsid exhibits an unusual architecture in which the viral DNA, probably in the form of a nucleoprotein filament, wraps around the longitudinal axis of the virion in a plane to form a multilayered disk-like structure with a central hole, and 16 of these structures are stacked to generate a spool-like capsid. SEV1 harbors a linear double-stranded DNA genome of ∼23 kb, which encodes 38 predicted open reading frames (ORFs). Among the few ORFs with a putative function is a gene encoding a protein-primed DNA polymerase. Sixfold symmetrical virus-associated pyramids (VAPs) appear on the surface of the SEV1-infected cells, which are ruptured to allow the formation of a hexagonal opening and subsequent release of the progeny virus particles. Notably, the SEV1 virions acquire the lipid membrane in the cytoplasm of the host cell. The lipid composition of the viral envelope correlates with that of the cell membrane. These results suggest the use of a unique mechanism by SEV1 in membrane biogenesis.IMPORTANCEInvestigation of archaeal viruses has greatly expanded our knowledge of the virosphere and its role in the evolution of life. Here we show thatSulfolobus ellipsoid virus 1(SEV1), an archaeal virus isolated from a hot spring in Costa Rica, exhibits a novel viral shape and an unusual capsid architecture. The SEV1 DNA wraps multiple times in a plane around the longitudinal axis of the virion to form a disk-like structure, and 16 of these structures are stacked to generate a spool-like capsid. The virus acquires its envelope intracellularly and exits the host cell by creating a hexagonal hole on the host cell surface. These results shed significant light on the diversity of viral morphogenesis.

Isolation and characterization of glioblastoma nuclei and chromosomes in the lyophilized state

1971 ◽  
Vol 34 (3) ◽  
pp. 301-309 ◽  
Author(s):  
Wolff M. Kirsch ◽  
Demoy Schulz ◽  
Paul Nakane ◽  
Robert Lasher ◽  
Tadami Yamamoto
Keyword(s):  
Water Soluble ◽  
High Yield ◽  
Nonaqueous Media ◽  
Biosynthetic Activity ◽  
Content Type ◽  
Isolation And Characterization ◽  
Subcellular Organelle ◽  
Fine Print

✓ Intact lyophilized nuclei and chromosomes were obtained from glioblastomas or brain, either in situ or in culture, by freezing at −156°C, drying at −25°C, and mechanical disassociation in glycerol at 2°C. Nuclear or chromosomal isolation was accomplished in hygroscopic nonaqueous media of high density. The method gave homogeneous nuclear and chromosomal preparations in high yield with preservation of labile, water-soluble constituents and residual biosynthetic activity. Unique opportunities for quantitative cytochemical studies at the level of the subcellular organelle are made available by the method.

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