scholarly journals Diversity, taxonomy and evolution of archaeal viruses of the class Caudoviricetes

2021 ◽  
Author(s):  
Ying Liu ◽  
Tatiana A. Demina ◽  
Simon Roux ◽  
Pakorn Aiewsakun ◽  
Darius Kazlauskas ◽  
...  
Keyword(s):  
Host Range ◽  
Defense Mechanisms ◽  
Halophilic Archaea ◽  
Ecological Impacts ◽  
Tail Fiber ◽  
Range Analysis ◽  
Host Interactions ◽  
Double Stranded Dna ◽  
Anoxic Environments ◽  
Archaeal Viruses

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.

scholarly journals Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes

PLoS Biology ◽  
2021 ◽  
Vol 19 (11) ◽  
pp. e3001442
Author(s):  
Ying Liu ◽  
Tatiana A. Demina ◽  
Simon Roux ◽  
Pakorn Aiewsakun ◽  
Darius Kazlauskas ◽  
...  
Keyword(s):  
Host Range ◽  
Defense Mechanisms ◽  
Halophilic Archaea ◽  
Ecological Impacts ◽  
Tail Fiber ◽  
Range Analysis ◽  
Host Interactions ◽  
Double Stranded Dna ◽  
Anoxic Environments ◽  
Archaeal Viruses

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 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 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.

scholarly journals His1, an Archaeal Virus of theFuselloviridae Family That Infects Haloarcula hispanica

1998 ◽  
Vol 72 (11) ◽  
pp. 9392-9395 ◽  
Author(s):  
Carolyn Bath ◽  
Michael L. Dyall-Smith
Keyword(s):  
Halophilic Archaea ◽  
Archaeal Virus ◽  
Extreme Thermophiles ◽  
Southeastern Australia ◽  
Double Stranded Dna ◽  
Archaeal Viruses ◽  
Low Salt ◽  
Extremely Halophilic Archaea ◽  
Haloarcula Hispanica

ABSTRACT A novel archaeal virus, His1, was isolated from hypersaline waters in southeastern Australia. It was lytic, grew only on Haloarcula hispanica (titers of up to 1011 PFU/ml), and displayed a lemon-shaped morphology (74 by 44 nm) previously reported only for a virus of the extreme thermophiles (SSV1). The density of His1 was approximately 1.28 g/ml, similar to that of SSV1 (1.24 g/ml). Purified particles were resistant to low salt concentrations. The genome was linear, double-stranded DNA of 14.9 kb, similar to the genome of SSV1 (15.5 kb). Morphologically, this isolate clearly belongs to the recently proposed Fuselloviridae family of archaeal viruses. It is the first member of this family from the extremely halophilic archaea, and its host, H. hispanica, can be readily manipulated genetically.

scholarly journals Viral Host Range database, an online tool for recording, analyzing and disseminating virus-host interactions

2021 ◽  
Author(s):  
Quentin Lamy-Besnier ◽  
Bryan Brancotte ◽  
Hervé Ménager ◽  
Laurent Debarbieux
Keyword(s):  
Host Range ◽  
Source Code ◽  
Range Data ◽  
Web Based ◽  
Online Tool ◽  
Experimental Host ◽  
Living World ◽  
Host Interactions ◽  
Experimental Host Range ◽  
Viral Host Range

Abstract Motivation Viruses are ubiquitous in the living world, and their ability to infect more than one host defines their host range. However, information about which virus infects which host, and about which host is infected by which virus, is not readily available. Results We developed a web-based tool called the Viral Host Range database to record, analyze and disseminate experimental host range data for viruses infecting archaea, bacteria and eukaryotes. Availability The ViralHostRangeDB application is available from https://viralhostrangedb.pasteur.cloud. Its source code is freely available from the Gitlab hub of Institut Pasteur (https://gitlab.pasteur.fr/hub/viralhostrangedb).

scholarly journals Host Range Expansion of Pseudomonas Virus LUZ7 Is Driven by a Conserved Tail Fiber Mutation

PHAGE ◽  
2020 ◽  
Vol 1 (2) ◽  
pp. 87-90 ◽  
Author(s):  
Maarten Boon ◽  
Dominique Holtappels ◽  
Cédric Lood ◽  
Vera van Noort ◽  
Rob Lavigne
Keyword(s):  
Host Range ◽  
Range Expansion ◽  
Tail Fiber ◽  
Host Range Expansion

scholarly journals Efficiency of Phage φ6 for Biocontrol of Pseudomonas syringae pv. syringae: An in Vitro Preliminary Study

2019 ◽  
Vol 7 (9) ◽  
pp. 286 ◽  
Author(s):  
Larindja A. M. Pinheiro ◽  
Carla Pereira ◽  
Carolina Frazão ◽  
Victor M. Balcão ◽  
Adelaide Almeida
Keyword(s):  
Solar Radiation ◽  
Host Range ◽  
Pseudomonas Syringae ◽  
Bacterial Resistance ◽  
Phage Therapy ◽  
Bacterial Species ◽  
Fruit Trees ◽  
Range Analysis ◽  
Maximum Reduction

Pseudomonas syringae is a plant-associated bacterial species that has been divided into more than 60 pathovars, with the Pseudomonas syringae pv. syringae being the main causative agent of diseases in a wide variety of fruit trees. The most common treatments for biocontrol of P. syringae pv. syringae infections has involved copper derivatives and/or antibiotics. However, these treatments should be avoided due to their high toxicity to the environment and promotion of bacterial resistance. Therefore, it is essential to search for new approaches for controlling P. syringae pv. syringae. Phage therapy can be a useful alternative tool to the conventional treatments to control P. syringae pv. syringae infections in plants. In the present study, the efficacy of bacteriophage (or phage) φ6 (a commercially available phage) was evaluated in the control of P. syringae pv. syringae. As the plants are exposed to the natural variability of physical and chemical parameters, the influence of pH, temperature, solar radiation and UV-B irradiation on phage φ6 viability was also evaluated in order to develop an effective phage therapy protocol. The host range analysis revealed that the phage, besides its host (P. syringae pv. syringae), also infects the Pseudomonas syringae pv. actinidiae CRA-FRU 12.54 and P. syringae pv. actinidiae CRA-FRU 14.10 strains, not infecting strains from the other tested species. Both multiplicities of infection (MOIs) tested, 1 and 100, were effective to inactivate the bacterium, but the MOI 1 (maximum reduction of 3.9 log CFU/mL) was more effective than MOI 100 (maximum reduction of 2.6 log CFU/mL). The viability of phage φ6 was mostly affected by exposure to UV-B irradiation (decrease of 7.3 log PFU/mL after 8 h), exposure to solar radiation (maximum reduction of 2.1 PFU/mL after 6 h), and high temperatures (decrease of 8.5 PFU/mL after 6 days at 37 °C, but a decrease of only 2.0 log PFU/mL after 67 days at 15 °C and 25 °C). The host range, high bacterial control and low rates of development of phage-resistant bacterial clones (1.20 × 10−3) suggest that this phage can be used to control P. syringae pv. syringae infections in plants, but also to control infections by P. syringae pv. actinidiae, the causal agent of bacterial canker of kiwifruit. Although the stability of phage φ6 was affected by UV-B and solar radiation, this can be overcome by the application of phage suspensions at the end of the day or at night.

scholarly journals A Spotlight on Viruses—Application of Click Chemistry to Visualize Virus-Cell Interactions

Molecules ◽  
2019 ◽  
Vol 24 (3) ◽  
pp. 481 ◽  
Author(s):  
Thorsten Müller ◽  
Volkan Sakin ◽  
Barbara Müller
Keyword(s):  
Click Chemistry ◽  
Defense Mechanisms ◽  
Fluorescent Labeling ◽  
Cell Interactions ◽  
Fluorescent Label ◽  
Host Interactions ◽  
Future Challenges ◽  
Genetic Code Expansion ◽  
Single Virus Tracking ◽  
Microscopy Techniques

The replication of a virus within its host cell involves numerous interactions between viral and cellular factors, which have to be tightly controlled in space and time. The intricate interplay between viral exploitation of cellular pathways and the intrinsic host defense mechanisms is difficult to unravel by traditional bulk approaches. In recent years, novel fluorescence microscopy techniques and single virus tracking have transformed the investigation of dynamic virus-host interactions. A prerequisite for the application of these imaging-based methods is the attachment of a fluorescent label to the structure of interest. However, their small size, limited coding capacity and multifunctional proteins render viruses particularly challenging targets for fluorescent labeling approaches. Click chemistry in conjunction with genetic code expansion provides virologists with a novel toolbox for site-specific, minimally invasive labeling of virion components, whose potential has just recently begun to be exploited. Here, we summarize recent achievements, current developments and future challenges for the labeling of viral nucleic acids, proteins, glycoproteins or lipids using click chemistry in order to study dynamic processes in virus-cell interactions.

scholarly journals A Novel Benthic Phage Infecting Shewanella with Strong Replication Ability

Viruses ◽  
2019 ◽  
Vol 11 (11) ◽  
pp. 1081 ◽  
Author(s):  
Zengmeng Wang ◽  
Jiulong Zhao ◽  
Long Wang ◽  
Chengcheng Li ◽  
Jianhui Liu ◽  
...  
Keyword(s):  
Burst Size ◽  
Coastal Sediments ◽  
The Yellow Sea ◽  
Comparative Genomic ◽  
Lytic Phage ◽  
Host Interactions ◽  
Metabolic Genes ◽  
Double Stranded Dna ◽  
Auxiliary Metabolic Genes ◽  
Structure Assembly

The coastal sediments were considered to contain diverse phages playing important roles in driving biogeochemical cycles based on genetic analysis. However, till now, benthic phages in coastal sediments were very rarely isolated, which largely limits our understanding of their biological characteristics. Here, we describe a novel lytic phage (named Shewanella phage S0112) isolated from the coastal sediments of the Yellow Sea infecting a sediment bacterium of the genus Shewanella. The phage has a very high replication capability, with the burst size of ca. 1170 phage particles per infected cell, which is 5–10 times higher than that of most phages isolated before. Meanwhile, the latent period of this phage is relatively longer, which might ensure adequate time for phage replication. The phage has a double-stranded DNA genome comprising 62,286 bp with 102 ORFs, ca. 60% of which are functionally unknown. The expression products of 16 ORF genes, mainly structural proteins, were identified by LC-MS/MS analysis. Besides the general DNA metabolism and structure assembly genes in the phage genome, there is a cluster of auxiliary metabolic genes that may be involved in 7-cyano-7-deazaguanine (preQ0) biosynthesis. Meanwhile, a pyrophosphohydrolase (MazG) gene being considered as a regulator of programmed cell death or involving in host stringer responses is inserted in this gene cluster. Comparative genomic and phylogenetic analysis both revealed a great novelty of phage S0112. This study represents the first report of a benthic phage infecting Shewanella, which also sheds light on the phage–host interactions in coastal sediments.

scholarly journals Host Range of Bacteriophages Against a World-Wide Collection of Erwinia amylovora Determined Using a Quantitative PCR Assay

Viruses ◽  
2019 ◽  
Vol 11 (10) ◽  
pp. 910 ◽  
Author(s):  
Gayder ◽  
Parcey ◽  
Castle ◽  
Svircev
Keyword(s):  
Host Range ◽  
Erwinia Amylovora ◽  
Plaque Assay ◽  
Infection Process ◽  
Broad Host Range ◽  
Range Data ◽  
Strongly Correlated ◽  
Range Analysis ◽  
Genome Copy Number ◽  
Phage Production

Erwinia amylovora is a globally devastating pathogen of apple, pear, and other Rosaceous plants. The use of lytic bacteriophages for disease management continues to garner attention as a possible supplement or alternative to antibiotics. A quantitative productive host range was established for 10 Erwinia phages using 106 wild type global isolates of E. amylovora, and the closely related Erwinia pyrifoliae, to investigate the potential regional efficacy of these phages within a biopesticide. Each host was individually infected with each of the 10 Erwinia phages and phage production after 8 h incubation was measured using quantitative real time PCR (qPCR) in conjunction with a standardized plasmid. PCR amplicons for all phages used in the study were incorporated into a single plasmid, allowing standardized quantification of the phage genome copy number after the infection process. Nine of the tested phages exhibited a broad host range, replicating their genomes by at least one log in over 88% of tested hosts. Also, every Amygdaloideae infecting E. amylovora host was able to increase at least one phage by three logs. Bacterial hosts isolated in western North America were less susceptible to most phages, as the mean genomic titre produced dropped by nearly two logs, and this phenomenon was strongly correlated to the amount of exopolysaccharide produced by the host. This method of host range analysis is faster and requires less effort than traditional plaque assay techniques, and the resulting quantitative data highlight subtle differences in phage host preference not observable with typical plaque-based host range assays. These quantitative host range data will be useful to determine which phages should be incorporated into a phage-mediated biocontrol formulation to be tested for regional and universal control of E. amylovora.

scholarly journals Diversity and Host Specificity Revealed by Biological Characterization and Whole Genome Sequencing of Bacteriophages Infecting Salmonella enterica

Viruses ◽  
2019 ◽  
Vol 11 (9) ◽  
pp. 854 ◽  
Author(s):  
Fong ◽  
Tremblay ◽  
Delaquis ◽  
Goodridge ◽  
Levesque ◽  
...  
Keyword(s):  
Host Range ◽  
Salmonella Enterica ◽  
Nucleotide Identity ◽  
Comparative Genomic ◽  
Broad Host Range ◽  
Natural Environments ◽  
Host Interactions ◽  
Knowledge Framework ◽  
Isolation And Characterization ◽  
Opportunistic Human Pathogen

Phages infecting members of the opportunistic human pathogen, Salmonella enterica, are widespread in natural environments and offer a potential source of agents that could be used for controlling populations of this bacterium; yet, relatively little is known about these phages. Here we describe the isolation and characterization of 45 phages of Salmonella enterica from disparate geographic locations within British Columbia, Canada. Host-range profiling revealed host-specific patterns of susceptibility and resistance, with several phages identified that have a broad-host range (i.e., able to lyse >40% of bacterial hosts tested). One phage in particular, SE13, is able to lyse 51 out of the 61 Salmonella strains tested. Comparative genomic analyses also revealed an abundance of sequence diversity in the sequenced phages. Alignment of the genomes grouped the phages into 12 clusters with three singletons. Phages within certain clusters exhibited extraordinarily high genome homology (>98% nucleotide identity), yet between clusters, genomes exhibited a span of diversity (<50% nucleotide identity). Alignment of the major capsid protein also supported the clustering pattern observed with alignment of the whole genomes. We further observed associations between genomic relatedness and the site of isolation, as well as genetic elements related to DNA metabolism and host virulence. Our data support the knowledge framework for phage diversity and phage–host interactions that are required for developing phage-based applications for various sectors, including biocontrol, detection and typing.

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