scholarly journals Targeted diversity generation by intraterrestrial archaea and archaeal viruses

2015 ◽  
Vol 6 (1) ◽  
Author(s):  
Blair G. Paul ◽  
Sarah C. Bagby ◽  
Elizabeth Czornyj ◽  
Diego Arambula ◽  
Sumit Handa ◽  
...  
Keyword(s):  
Archaeal Viruses

scholarly journals Prokaryotic virus host predictor: a Gaussian model for host prediction of prokaryotic viruses in metagenomics

BMC Biology ◽  
2021 ◽  
Vol 19 (1) ◽  
Author(s):  
Congyu Lu ◽  
Zheng Zhang ◽  
Zena Cai ◽  
Zhaozhong Zhu ◽  
Ye Qiu ◽  
...  
Keyword(s):  
Prediction Accuracy ◽  
Functional Characterization ◽  
Gaussian Model ◽  
Software Tool ◽  
Biological Properties ◽  
Rapid Identification ◽  
Taxonomic Assignment ◽  
Genus Level ◽  
Alignment Free ◽  
Archaeal Viruses

Abstract Background Viruses are ubiquitous biological entities, estimated to be the largest reservoirs of unexplored genetic diversity on Earth. Full functional characterization and annotation of newly discovered viruses requires tools to enable taxonomic assignment, the range of hosts, and biological properties of the virus. Here we focus on prokaryotic viruses, which include phages and archaeal viruses, and for which identifying the viral host is an essential step in characterizing the virus, as the virus relies on the host for survival. Currently, the method for determining the viral host is either to culture the virus, which is low-throughput, time-consuming, and expensive, or to computationally predict the viral hosts, which needs improvements at both accuracy and usability. Here we develop a Gaussian model to predict hosts for prokaryotic viruses with better performances than previous computational methods. Results We present here Prokaryotic virus Host Predictor (PHP), a software tool using a Gaussian model, to predict hosts for prokaryotic viruses using the differences of k-mer frequencies between viral and host genomic sequences as features. PHP gave a host prediction accuracy of 34% (genus level) on the VirHostMatcher benchmark dataset and a host prediction accuracy of 35% (genus level) on a new dataset containing 671 viruses and 60,105 prokaryotic genomes. The prediction accuracy exceeded that of two alignment-free methods (VirHostMatcher and WIsH, 28–34%, genus level). PHP also outperformed these two alignment-free methods much (24–38% vs 18–20%, genus level) when predicting hosts for prokaryotic viruses which cannot be predicted by the BLAST-based or the CRISPR-spacer-based methods alone. Requiring a minimal score for making predictions (thresholding) and taking the consensus of the top 30 predictions further improved the host prediction accuracy of PHP. Conclusions The Prokaryotic virus Host Predictor software tool provides an intuitive and user-friendly API for the Gaussian model described herein. This work will facilitate the rapid identification of hosts for newly identified prokaryotic viruses in metagenomic studies.

Exploitation of plant and archaeal viruses in bionanotechnology

2009 ◽  
Vol 37 (4) ◽  
pp. 665-670 ◽  
Author(s):  
David J. Evans
Keyword(s):  
The Body ◽  
Layer By Layer ◽  
Archaeal Virus ◽  
Sulfolobus Islandicus ◽  
Naturally Occurring ◽  
Archaeal Viruses ◽  
Nanobuilding Blocks ◽  
Multiple Copies ◽  
Site Selective ◽  
Virion Surface

CPMV (cowpea mosaic virus), a plant virus, is a naturally occurring sphere-like nanoparticle, and is used as a synthon and/or template in bionanoscience. The virions formed by CPMV can be regarded as programmable nanobuilding blocks with a diameter of ∼30 nm. A range of molecules have been attached to this viral nanoscaffold, yielding stable nanoparticles that display multiple copies of the desired molecule. It has been shown that, in addition to surface amine groups, surface carboxy groups are also addressable, and a procedure has been developed that enables introduction of reactive thiols at the virion surface that avoids virus aggregation. Furthermore, the virions can be functionalized to form electroactive nanoparticles. Methods for the construction of arrays and multilayers, using a layer-by-layer approach, have been established. As proof of concept, for example, CPMV particles have been immobilized on surfaces and arranged in defined layers. Engineered variants of CPMV can be used as templates for mineralization with, for example, silica to give monodisperse robust silica nanoparticles of ∼32 nm. SIRV2 (Sulfolobus islandicus rod-shaped virus 2), is a robust archaeal virus, resistant to high temperature and low pH. SIRV2 can act as a template for site-selective and spatially controlled chemical modification. Both the ends and the body of the virus, or the ends only, can be chemically addressed; SIRV2 can be regarded as a structurally unique nanobuilding block.

scholarly journals Unique viruses that infect Archaea related to eukaryotes

2021 ◽  
Author(s):  
Ian M Rambo ◽  
Valerie De Anda ◽  
Marguerite V Langwig ◽  
Brett J Baker
Keyword(s):  
Transcriptional Regulation ◽  
Deep Sea ◽  
Structural Proteins ◽  
Genome Replication ◽  
Dna Viruses ◽  
Viral Genomes ◽  
Archaeal Viruses ◽  
Hydrothermal Sediments ◽  
Nucleocytoplasmic Large Dna Viruses ◽  
Globally Distributed

Asgard archaea are newly described microbes that are related to eukaryotes. Asgards are diverse and globally distributed, however, their viruses have not been described. Here we characterize seven viral genomes that infected Lokiarchaeota, Helarchaeota, and Thorarchaeota in deep-sea hydrothermal sediments. These viruses code for structural proteins similar to those in Caudovirales, as well as proteins distinct from those described in archaeal viruses. They also have genes common in eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs), and are predicted to be capable of semi-autonomous genome replication, repair, epigenetic modifications, and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. This first glimpse of Asgard viruses reveals they have features of both prokaryotic and eukaryotic viruses, and provides insights into their roles in the ecology and evolution of these globally distributed microbes.

scholarly journals ORF4 of the Temperate Archaeal Virus SNJ1 Governs the Lysis-Lysogeny Switch and Superinfection Immunity

2020 ◽  
Vol 94 (16) ◽  
Author(s):  
Beibei Chen ◽  
Zhao Chen ◽  
Yuchen Wang ◽  
Han Gong ◽  
Linshan Sima ◽  
...  
Keyword(s):  
Life Cycle ◽  
Bioinformatic Analysis ◽  
Model System ◽  
Life Cycles ◽  
Host Cells ◽  
Biological Functions ◽  
Mechanistic Studies ◽  
Cultivation Conditions ◽  
Archaeal Virus ◽  
Archaeal Viruses

ABSTRACT Recent environmental and metagenomic studies have considerably increased the repertoire of archaeal viruses and suggested that they play important roles in nutrient cycling in the biosphere. However, very little is known about how they regulate their life cycles and interact with their hosts. Here, we report that the life cycle of the temperate haloarchaeal virus SNJ1 is controlled by the product ORF4, a small protein belonging to the antitoxin MazE superfamily. We show that ORF4 controls the lysis-lysogeny switch of SNJ1 and mediates superinfection immunity by repression of genomic DNA replication of the superinfecting viruses. Bioinformatic analysis shows that ORF4 is highly conserved in two SNJ1-like proviruses, suggesting that the mechanisms for lysis-lysogeny switch and superinfection immunity are conserved in this group of viruses. As the lysis-lysogeny switch and superinfection immunity of archaeal viruses have been poorly studied, we suggest that SNJ1 could serve as a model system to study these processes. IMPORTANCE Archaeal viruses are important parts of the virosphere. Understanding how they regulate their life cycles and interact with host cells provide crucial insights into their biological functions and the evolutionary histories of viruses. However, mechanistic studies of the life cycle of archaeal viruses are scarce due to a lack of genetic tools and demanding cultivation conditions. Here, we discover that the temperate haloarchaeal virus SNJ1, which infects Natrinema sp. strain J7, employs a lysis-lysogeny switch and establishes superinfection immunity like bacteriophages. We show that its ORF4 is critical for both processes and acts as a repressor of the replication of SNJ1. These results establish ORF4 as a master regulator of SNJ1 life cycle and provides novel insights on the regulation of life cycles by temperate archaeal viruses and on their interactions with host cells.

New archaeal viruses discovered by metagenomic analysis of viral communities in enrichment cultures

2019 ◽  
Vol 21 (6) ◽  
pp. 2002-2014 ◽  
Author(s):  
Ying Liu ◽  
David Brandt ◽  
Sonoko Ishino ◽  
Yoshizumi Ishino ◽  
Eugene V. Koonin ◽  
...  
Keyword(s):  
Metagenomic Analysis ◽  
Enrichment Cultures ◽  
Archaeal Viruses ◽  
Viral Communities

scholarly journals Particle Assembly and Ultrastructural Features Associated with Replication of the Lytic Archaeal Virus Sulfolobus Turreted Icosahedral Virus

2009 ◽  
Vol 83 (12) ◽  
pp. 5964-5970 ◽  
Author(s):  
Susan K. Brumfield ◽  
Alice C. Ortmann ◽  
Vincent Ruigrok ◽  
Peter Suci ◽  
Trevor Douglas ◽  
...  
Keyword(s):  
Time Course ◽  
Plaque Assay ◽  
Ultrastructural Changes ◽  
Progeny Virus ◽  
Particle Assembly ◽  
Virus Particles ◽  
Transmission Electron ◽  
Archaeal Viruses ◽  
Infected Cells ◽  
Sulfolobus Turreted Icosahedral Virus

ABSTRACT Little is known about the replication cycle of archaeal viruses. We have investigated the ultrastructural changes of Sulfolobus solfataricus P2 associated with infection by Sulfolobus turreted icosahedral virus (STIV). A time course of a near synchronous STIV infection was analyzed using both scanning and transmission electron microscopy. Assembly of STIV particles, including particles lacking DNA, was observed within cells, and fully assembled STIV particles were visible by 30 h postinfection (hpi). STIV was determined to be a lytic virus, causing cell disruption beginning at 30 hpi. Prior to cell lysis, virus infection resulted in the formation of pyramid-like projections from the cell surface. These projections, which have not been documented in any other host-virus system, appeared to be caused by the protrusion of the cell membrane beyond the bordering S-layer. These structures are thought to be sites at which progeny virus particles are released from infected cells. Based on these observations of lysis, a plaque assay was developed for STIV. From these studies we propose an overall assembly model for STIV.

Distribution of CRISPR spacer matches in viruses and plasmids of crenarchaeal acidothermophiles and implications for their inhibitory mechanism

2009 ◽  
Vol 37 (1) ◽  
pp. 23-28 ◽  
Author(s):  
Shiraz Ali Shah ◽  
Niels R. Hansen ◽  
Roger A. Garrett
Keyword(s):  
Plasmid Dna ◽  
Genomic Dna ◽  
Inhibitory Mechanism ◽  
Archaeal Viruses ◽  
Extrachromosomal Elements ◽  
Dna Strand ◽  
High Level

Transcripts from spacer sequences within chromosomal repeat clusters [CRISPRs (clusters of regularly interspaced palindromic repeats)] from archaea have been implicated in inhibiting or regulating the propagation of archaeal viruses and plasmids. For the crenarchaeal thermoacidophiles, the chromosomal spacers show a high level of matches (∼30%) with viral or plasmid genomes. Moreover, their distribution along the virus/plasmid genomes, as well as their DNA strand specificity, appear to be random. This is consistent with the hypothesis that chromosomal spacers are taken up directly and randomly from virus and plasmid DNA and that the spacer transcripts target the genomic DNA of the extrachromosomal elements and not their transcripts.

Biogeographical diversity of archaeal viruses

2010 ◽  
pp. 131-144 ◽  
Author(s):  
Kenneth M. Stedman ◽  
Adam Clore ◽  
Yannick Combet-Blanc
Keyword(s):  
Archaeal Viruses

scholarly journals Xenogeneic modulation of the ClpCP protease of Bacillus subtilis by a phage-encoded adaptor-like protein

2019 ◽  
Vol 294 (46) ◽  
pp. 17501-17511 ◽  
Author(s):  
Nancy Mulvenna ◽  
Ingo Hantke ◽  
Lynn Burchell ◽  
Sophie Nicod ◽  
David Bell ◽  
...  
Keyword(s):  
Bacillus Subtilis ◽  
Gene Products ◽  
Bacterial Host ◽  
Systematic Analysis ◽  
Phage Gene ◽  
Cellular Processes ◽  
Bacteriophage Infection ◽  
Archaeal Viruses ◽  
Cytotoxic Proteins ◽  
Cellular Pathways

Like eukaryotic and archaeal viruses, which coopt the host's cellular pathways for their replication, bacteriophages have evolved strategies to alter the metabolism of their bacterial host. SPO1 bacteriophage infection of Bacillus subtilis results in comprehensive remodeling of cellular processes, leading to conversion of the bacterial cell into a factory for phage progeny production. A cluster of 26 genes in the SPO1 genome, called the host takeover module, encodes for potentially cytotoxic proteins that specifically shut down various processes in the bacterial host, including transcription, DNA synthesis, and cell division. However, the properties and bacterial targets of many genes of the SPO1 host takeover module remain elusive. Through a systematic analysis of gene products encoded by the SPO1 host takeover module, here we identified eight gene products that attenuated B. subtilis growth. Of the eight phage gene products that attenuated bacterial growth, a 25-kDa protein called Gp53 was shown to interact with the AAA+ chaperone protein ClpC of the ClpCP protease of B. subtilis. Our results further reveal that Gp53 is a phage-encoded adaptor-like protein that modulates the activity of the ClpCP protease to enable efficient SPO1 phage progeny development. In summary, our findings indicate that the bacterial ClpCP protease is the target of xenogeneic (dys)regulation by a SPO1 phage–derived factor and add Gp53 to the list of antibacterial products that target bacterial protein degradation and therefore may have utility for the development of novel antibacterial agents.

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