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Special Issue "Viruses of Microbes"

A special issue of Viruses (ISSN 1999-4915). This special issue belongs to the section "Bacterial Viruses".

Deadline for manuscript submissions: closed (31 March 2017)

Special Issue Editors

Guest Editor
Dr. Tessa E.F. Quax

University Freiburg, Institute for Biology II - Microbiology Molecular Biology of Archaea, Schänzlestrasse 1, 79104 Freiburg, Germany
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Interests: archaeal viruses; molecular biology of archaea; archaeal membrane biology
Guest Editor
Dr. Matthias G. Fischer

Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research, Heidelberg, Germany
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Interests: giant DNA viruses; virophages; protist viruses; virus-host interactions; virus evolution
Guest Editor
Dr. Laurent Debarbieux

Department of Microbiology, Institut Pasteur, Paris, France
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Interests: bacteriophage biology; bacteriophage-host interactions; phage therapy

Special Issue Information

Dear Colleagues,

The International Society for Viruses of Microbes (ISVM) represents large scientific community studying viruses of archaea, bacteria, protists and fungi. One of its activities is a biannual multidisciplinary meeting, which covers the full range of current developments in the field of viruses of microbes, from structural biology to ecology and from fundamental to applied research.

In the Viruses of Microbes Special Issues published in Viruses, we hope to collect series of research articles which will reflect the full diversity of this field with current and future trends of fundamental and applied research.

Dr. Tessa E.F. Quax
Dr. Matthias G. Fischer
Dr. Laurent Debarbieux
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Viruses is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1500 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Biology of microbial viruses
  • Virus host interactions
  • Molecular mechanisms
  • Applications of viruses (biotechnology and medical)

Published Papers (8 papers)

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Research

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Open AccessArticle The Transmembrane Morphogenesis Protein gp1 of Filamentous Phages Contains Walker A and Walker B Motifs Essential for Phage Assembly
Viruses 2017, 9(4), 73; doi:10.3390/v9040073
Received: 8 February 2017 / Revised: 29 March 2017 / Accepted: 4 April 2017 / Published: 9 April 2017
Cited by 1 | PDF Full-text (1827 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
In contrast to lytic phages, filamentous phages are assembled in the inner membrane and secreted across the bacterial envelope without killing the host. For assembly and extrusion of the phage across the host cell wall, filamentous phages code for membrane-embedded morphogenesis proteins. In
[...] Read more.
In contrast to lytic phages, filamentous phages are assembled in the inner membrane and secreted across the bacterial envelope without killing the host. For assembly and extrusion of the phage across the host cell wall, filamentous phages code for membrane-embedded morphogenesis proteins. In the outer membrane of Escherichia coli, the protein gp4 forms a pore-like structure, while gp1 and gp11 form a complex in the inner membrane of the host. By comparing sequences with other filamentous phages, we identified putative Walker A and B motifs in gp1 with a conserved lysine in the Walker A motif (K14), and a glutamic and aspartic acid in the Walker B motif (D88, E89). In this work we demonstrate that both, Walker A and Walker B, are essential for phage production. The crucial role of these key residues suggests that gp1 might be a molecular motor driving phage assembly. We further identified essential residues for the function of the assembly complex. Mutations in three out of six cysteine residues abolish phage production. Similarly, two out of six conserved glycine residues are crucial for gp1 function. We hypothesise that the residues represent molecular hinges allowing domain movement for nucleotide binding and phage assembly. Full article
(This article belongs to the Special Issue Viruses of Microbes)
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Open AccessCommunication How to Name and Classify Your Phage: An Informal Guide
Viruses 2017, 9(4), 70; doi:10.3390/v9040070
Received: 24 February 2017 / Revised: 28 March 2017 / Accepted: 28 March 2017 / Published: 3 April 2017
PDF Full-text (363 KB) | HTML Full-text | XML Full-text
Abstract
With this informal guide, we try to assist both new and experienced phage researchers through two important stages that follow phage discovery; that is, naming and classification. Providing an appropriate name for a bacteriophage is not as trivial as it sounds, and the
[...] Read more.
With this informal guide, we try to assist both new and experienced phage researchers through two important stages that follow phage discovery; that is, naming and classification. Providing an appropriate name for a bacteriophage is not as trivial as it sounds, and the effects might be long-lasting in databases and in official taxon names. Phage classification is the responsibility of the Bacterial and Archaeal Viruses Subcommittee (BAVS) of the International Committee on the Taxonomy of Viruses (ICTV). While the BAVS aims at providing a holistic approach to phage taxonomy, for individual researchers who have isolated and sequenced a new phage, this can be a little overwhelming. We are now providing these researchers with an informal guide to phage naming and classification, taking a “bottom-up” approach from the phage isolate level. Full article
(This article belongs to the Special Issue Viruses of Microbes)
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Open AccessArticle Phage Biodiversity in Artisanal Cheese Wheys Reflects the Complexity of the Fermentation Process
Viruses 2017, 9(3), 45; doi:10.3390/v9030045
Received: 3 February 2017 / Revised: 8 March 2017 / Accepted: 13 March 2017 / Published: 16 March 2017
PDF Full-text (1186 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Dairy fermentations constitute a perfect “breeding ground” for bacteriophages infecting starter cultures, particularly strains of Lactococcus lactis. In modern fermentations, these phages typically belong to one of three groups, i.e., the 936, P335, and c2 phage groups. Traditional production methods present fewer chemical
[...] Read more.
Dairy fermentations constitute a perfect “breeding ground” for bacteriophages infecting starter cultures, particularly strains of Lactococcus lactis. In modern fermentations, these phages typically belong to one of three groups, i.e., the 936, P335, and c2 phage groups. Traditional production methods present fewer chemical and physical barriers to phage proliferation compared to modern production systems, while the starter cultures used are typically complex, variable, and undefined. In the current study, a variety of cheese whey, animal-derived rennet, and vat swab samples from artisanal cheeses produced in Sicily were analysed for the presence of lactococcal phages to assess phage diversity in such environments. The complete genomes of 18 representative phage isolates were sequenced, allowing the identification of 10 lactococcal 949 group phages, six P087 group phages, and two members of the 936 group phages. The genetic diversity of these isolates was examined using phylogenetic analysis as well as a focused analysis of the receptor binding proteins, which dictate specific interactions with the host-encoded receptor. Thermal treatments at 63 °C and 83 °C indicate that the 949 phages are particularly sensitive to thermal treatments, followed by the P087 and 936 isolates, which were shown to be much less sensitive to such treatments. This difference may explain the relatively low frequency of isolation of the so-called “rare” 949 and P087 group phages in modern fermentations. Full article
(This article belongs to the Special Issue Viruses of Microbes)
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Open AccessArticle Capsule-Targeting Depolymerase, Derived from Klebsiella KP36 Phage, as a Tool for the Development of Anti-Virulent Strategy
Viruses 2016, 8(12), 324; doi:10.3390/v8120324
Received: 22 September 2016 / Revised: 17 November 2016 / Accepted: 23 November 2016 / Published: 1 December 2016
Cited by 1 | PDF Full-text (4352 KB) | HTML Full-text | XML Full-text
Abstract
The rise of antibiotic-resistant Klebsiella pneumoniae, a leading nosocomial pathogen, prompts the need for alternative therapies. We have identified and characterized a novel depolymerase enzyme encoded by Klebsiella phage KP36 (depoKP36), from the Siphoviridae family. To gain insights into the catalytic and
[...] Read more.
The rise of antibiotic-resistant Klebsiella pneumoniae, a leading nosocomial pathogen, prompts the need for alternative therapies. We have identified and characterized a novel depolymerase enzyme encoded by Klebsiella phage KP36 (depoKP36), from the Siphoviridae family. To gain insights into the catalytic and structural features of depoKP36, we have recombinantly produced this protein of 93.4 kDa and showed that it is able to hydrolyze a crude exopolysaccharide of a K. pneumoniae host. Using in vitro and in vivo assays, we found that depoKP36 was also effective against a native capsule of clinical K. pneumoniae strains, representing the K63 type, and significantly inhibited Klebsiella-induced mortality of Galleria mellonella larvae in a time-dependent manner. DepoKP36 did not affect the antibiotic susceptibility of Klebsiella strains. The activity of this enzyme was retained in a broad range of pH values (4.0–7.0) and temperatures (up to 45 °C). Consistently, the circular dichroism (CD) spectroscopy revealed a highly stability with melting transition temperature (Tm) = 65 °C. In contrast to other phage tailspike proteins, this enzyme was susceptible to sodium dodecyl sulfate (SDS) denaturation and proteolytic cleavage. The structural studies in solution showed a trimeric arrangement with a high β-sheet content. Our findings identify depoKP36 as a suitable candidate for the development of new treatments for K. pneumoniae infections. Full article
(This article belongs to the Special Issue Viruses of Microbes)
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Open AccessArticle Two Novel Myoviruses from the North of Iraq Reveal Insights into Clostridium difficile Phage Diversity and Biology
Viruses 2016, 8(11), 310; doi:10.3390/v8110310
Received: 23 September 2016 / Revised: 3 November 2016 / Accepted: 8 November 2016 / Published: 16 November 2016
PDF Full-text (6501 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Bacteriophages (phages) are increasingly being explored as therapeutic agents to combat bacterial diseases, including Clostridium difficile infections. Therapeutic phages need to be able to efficiently target and kill a wide range of clinically relevant strains. While many phage groups have yet to be
[...] Read more.
Bacteriophages (phages) are increasingly being explored as therapeutic agents to combat bacterial diseases, including Clostridium difficile infections. Therapeutic phages need to be able to efficiently target and kill a wide range of clinically relevant strains. While many phage groups have yet to be investigated in detail, those with new and useful properties can potentially be identified when phages from newly studied geographies are characterised. Here, we report the isolation of C. difficile phages from soil samples from the north of Iraq. Two myoviruses, CDKM15 and CDKM9, were selected for detailed sequence analysis on the basis of their broad and potentially useful host range. CDKM9 infects 25/80 strains from 12/20 C. difficile ribotypes, and CDKM15 infects 20/80 strains from 9/20 ribotypes. Both phages can infect the clinically relevant ribotypes R027 and R001. Phylogenetic analysis based on whole genome sequencing revealed that the phages are genetically distinct from each other but closely related to other long-tailed myoviruses. A comparative genomic analysis revealed key differences in the genes predicted to encode for proteins involved in bacterial infection. Notably, CDKM15 carries a clustered regularly interspaced short palindromic repeat (CRISPR) array with spacers that are homologous to sequences in the CDKM9 genome and of phages from diverse localities. The findings presented suggest a possible shared evolutionary past for these phages and provides evidence of their widespread dispersal. Full article
(This article belongs to the Special Issue Viruses of Microbes)
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Review

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Open AccessFeature PaperReview Chloroviruses Have a Sweet Tooth
Viruses 2017, 9(4), 88; doi:10.3390/v9040088
Received: 17 March 2017 / Revised: 13 April 2017 / Accepted: 14 April 2017 / Published: 22 April 2017
PDF Full-text (1743 KB) | HTML Full-text | XML Full-text
Abstract
Chloroviruses are large double-stranded DNA (dsDNA) viruses that infect certain isolates of chlorella-like green algae. They contain up to approximately 400 protein-encoding genes and 16 transfer RNA (tRNA) genes. This review summarizes the unexpected finding that many of the chlorovirus genes encode proteins
[...] Read more.
Chloroviruses are large double-stranded DNA (dsDNA) viruses that infect certain isolates of chlorella-like green algae. They contain up to approximately 400 protein-encoding genes and 16 transfer RNA (tRNA) genes. This review summarizes the unexpected finding that many of the chlorovirus genes encode proteins involved in manipulating carbohydrates. These include enzymes involved in making extracellular polysaccharides, such as hyaluronan and chitin, enzymes that make nucleotide sugars, such as GDP-L-fucose and GDP-D-rhamnose and enzymes involved in the synthesis of glycans attached to the virus major capsid proteins. This latter process differs from that of all other glycoprotein containing viruses that traditionally use the host endoplasmic reticulum and Golgi machinery to synthesize and transfer the glycans. Full article
(This article belongs to the Special Issue Viruses of Microbes)
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Open AccessReview HCIV-1 and Other Tailless Icosahedral Internal Membrane-Containing Viruses of the Family Sphaerolipoviridae
Viruses 2017, 9(2), 32; doi:10.3390/v9020032
Received: 10 January 2017 / Revised: 10 January 2017 / Accepted: 13 February 2017 / Published: 18 February 2017
PDF Full-text (3242 KB) | HTML Full-text | XML Full-text
Abstract
Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus
[...] Read more.
Members of the virus family Sphaerolipoviridae include both archaeal viruses and bacteriophages that possess a tailless icosahedral capsid with an internal membrane. The genera Alpha- and Betasphaerolipovirus comprise viruses that infect halophilic euryarchaea, whereas viruses of thermophilic Thermus bacteria belong to the genus Gammasphaerolipovirus. Both sequence-based and structural clustering of the major capsid proteins and ATPases of sphaerolipoviruses yield three distinct clades corresponding to these three genera. Conserved virion architectural principles observed in sphaerolipoviruses suggest that these viruses belong to the PRD1-adenovirus structural lineage. Here we focus on archaeal alphasphaerolipoviruses and their related putative proviruses. The highest sequence similarities among alphasphaerolipoviruses are observed in the core structural elements of their virions: the two major capsid proteins, the major membrane protein, and a putative packaging ATPase. A recently described tailless icosahedral haloarchaeal virus, Haloarcula californiae icosahedral virus 1 (HCIV-1), has a double-stranded DNA genome and an internal membrane lining the capsid. HCIV-1 shares significant similarities with the other tailless icosahedral internal membrane-containing haloarchaeal viruses of the family Sphaerolipoviridae. The proposal to include a new virus species, Haloarcula virus HCIV1, into the genus Alphasphaerolipovirus was submitted to the International Committee on Taxonomy of Viruses (ICTV) in 2016. Full article
(This article belongs to the Special Issue Viruses of Microbes)
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Other

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Open AccessConference Report “French Phage Network”—Second Meeting Report
Viruses 2017, 9(4), 87; doi:10.3390/v9040087
Received: 29 March 2017 / Revised: 29 March 2017 / Accepted: 19 April 2017 / Published: 21 April 2017
PDF Full-text (907 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The study of bacteriophages (viruses of bacteria) includes a variety of approaches, such as structural biology, genetics, ecology, and evolution, with increasingly important implications for therapeutic and industrial uses. Researchers working with phages in France have recently established a network to facilitate the
[...] Read more.
The study of bacteriophages (viruses of bacteria) includes a variety of approaches, such as structural biology, genetics, ecology, and evolution, with increasingly important implications for therapeutic and industrial uses. Researchers working with phages in France have recently established a network to facilitate the exchange on complementary approaches, but also to engage new collaborations. Here, we provide a summary of the topics presented during the second meeting of the French Phage Network that took place in Marseille in November 2016 Full article
(This article belongs to the Special Issue Viruses of Microbes)
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