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Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes

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

Deadline for manuscript submissions: closed (31 December 2020) | Viewed by 55641

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Special Issue Editors

Dr. Tessa E.F. Quax

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Guest Editor

Biology of Archaea and Viruses, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, Groningen, The Netherlands
Interests: archaeal viruses; molecular biology of archaea; archaeal membrane biology
Special Issues, Collections and Topics in MDPI journals

Dr. Marianne De Paepe

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Micalis Institute, INRAE, Jouy-en-Josas, France
Interests: temperate phages; intestinal phages; phage genome evolution and mutation rates

Dr. Karin Holmfeldt

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Guest Editor

Department of Biology and Environmental Sciences, Linnaeus University, 391 82 Kalmar, Sweden
Interests: environmental virology; phage-host interactions; omics and bioinformatics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

We invite submissions to the special issue "Viruses of Microbes", which is associated with the 2021 meeting from the ISVM (International Society of Viruses of Microbes) and will be held in Guimarães, Portugal, in 2021. The central theme of the meeting and this special issue is “the latest conquests on viruses of microbes”. The issue intends to be a platform for the latest advances on research of microbial viruses, from ecology and evolution, to virus structure and function, and from virus-host interaction to biotechnology applications and phage therapy.

We specifically invite researchers studying viruses of all three domains of life to submit their work. We strongly believe that uniting these research and review papers will be of great interest to a wide-ranging audience that is concerned with both the fundamental and applied aspects of microbial viruses. In accordance with the ISVM 2021 meeting in Guimarães, the special issue will cover the following topics:

Ecology and evolution of microbial viruses
Virus structures and function
Virus-host interaction: overcoming cell barriers
Virus-host interaction: molecular mechanisms
Virus-host interaction: host defence and viral evasion mechanisms
Agro-food, veterinary and environmental biotechnology applications
Biotechnology applications in health care
Current state and latest developments of phage therapy

We hope to collect a series of research articles which will reflect the full diversity of this field with current and future trends of fundamental and applied research. ISVM members receive a 10% discount and a limited number of fee waivers is available. We would be happy if you contact us in advance by email about planned submissions.

Dr. Tessa E.F. Quax
Dr. Marianne De Paepe
Dr. Karin Holmfeldt
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 submissions that pass pre-check are 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 2600 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

Ecology and evolution of microbial viruses
Impact of microbial viruses on biochemical cycles
Virus structures and function
Virus-host interaction: overcoming cell barriers and molecular mechanisms
Host defence and viral evasion mechanisms
Agro-food, veterinary and environmental biotechnology applications
Biotechnology applications in health care
Phage therapy

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Related Special Issues

Viruses of Microbes in Viruses (20 articles)
Viruses of Microbes V: Biodiversity and Future Applications in Viruses (16 articles)
Viruses of Microbes 2022 in Viruses (4 articles)

Published Papers (12 papers)

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Editorial

Jump to: Research, Review

2 pages, 161 KiB

Open AccessEditorial

Viruses of Microbes 2020: The Latest Conquest on Viruses of Microbes

by Tessa E. F. Quax, Marianne De Paepe and Karin Holmfeldt

Viruses 2021, 13(5), 802; https://doi.org/10.3390/v13050802 - 30 Apr 2021

Viewed by 2120

Abstract

This Special Issue celebrates viruses of microbes: those viruses that infect archaea, bacteria and microbial eukaryotes [...] Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

Research

Jump to: Editorial, Review

19 pages, 4252 KiB

Open AccessArticle

First Description of a Temperate Bacteriophage (vB_FhiM_KIRK) of Francisella hispaniensis Strain 3523

by Kristin Köppen, Grisna I. Prensa, Kerstin Rydzewski, Hana Tlapák, Gudrun Holland and Klaus Heuner

Viruses 2021, 13(2), 327; https://doi.org/10.3390/v13020327 - 20 Feb 2021

Cited by 3 | Viewed by 2768

Abstract

Here we present the characterization of a Francisella bacteriophage (vB_FhiM_KIRK) including the morphology, the genome sequence and the induction of the prophage. The prophage sequence (FhaGI-1) has previously been identified in F. hispaniensis strain 3523. UV radiation induced the prophage to assemble phage particles consisting of an icosahedral head (~52 nm in diameter), a tail of up to 97 nm in length and a mean width of 9 nm. The double stranded genome of vB_FhiM_KIRK contains 51 open reading frames and is 34,259 bp in length. The genotypic and phylogenetic analysis indicated that this phage seems to belong to the Myoviridae family of bacteriophages. Under the conditions tested here, host cell (Francisella hispaniensis 3523) lysis activity of KIRK was very low, and the phage particles seem to be defective for infecting new bacterial cells. Nevertheless, recombinant KIRK DNA was able to integrate site-specifically into the genome of different Francisella species after DNA transformation. Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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15 pages, 2354 KiB

Open AccessArticle

Overexpression of the Bacteriophage T4 motB Gene Alters H-NS Dependent Repression of Specific Host DNA

by Jennifer Patterson-West, Chin-Hsien Tai, Bokyung Son, Meng-Lun Hsieh, James R. Iben and Deborah M. Hinton

Viruses 2021, 13(1), 84; https://doi.org/10.3390/v13010084 - 9 Jan 2021

Cited by 5 | Viewed by 2944

Abstract

The bacteriophage T4 early gene product MotB binds tightly but nonspecifically to DNA, copurifies with the host Nucleoid Associated Protein (NAP) H-NS in the presence of DNA and improves T4 fitness. However, the T4 transcriptome is not significantly affected by a motB knockdown. Here we have investigated the phylogeny of MotB and its predicted domains, how MotB and H-NS together interact with DNA, and how heterologous overexpression of motB impacts host gene expression. We find that motB is highly conserved among Tevenvirinae. Although the MotB sequence has no homology to proteins of known function, predicted structure homology searches suggest that MotB is composed of an N-terminal Kyprides-Onzonis-Woese (KOW) motif and a C-terminal DNA-binding domain of oligonucleotide/oligosaccharide (OB)-fold; either of which could provide MotB’s ability to bind DNA. DNase I footprinting demonstrates that MotB dramatically alters the interaction of H-NS with DNA in vitro. RNA-seq analyses indicate that expression of plasmid-borne motB up-regulates 75 host genes; no host genes are down-regulated. Approximately 1/3 of the up-regulated genes have previously been shown to be part of the H-NS regulon. Our results indicate that MotB provides a conserved function for Tevenvirinae and suggest a model in which MotB functions to alter the host transcriptome, possibly by changing the association of H-NS with the host DNA, which then leads to conditions that are more favorable for infection. Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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15 pages, 1886 KiB

Open AccessArticle

Transcriptional Landscape of Staphylococcus aureus Kayvirus Bacteriophage vB_SauM-515A1

by Maria Kornienko, Gleb Fisunov, Dmitry Bespiatykh, Nikita Kuptsov, Roman Gorodnichev, Ksenia Klimina, Eugene Kulikov, Elena Ilina, Andrey Letarov and Egor Shitikov

Viruses 2020, 12(11), 1320; https://doi.org/10.3390/v12111320 - 17 Nov 2020

Cited by 12 | Viewed by 3228

Abstract

The Twort-like myoviruses (Kayvirus genus) of S. aureus are promising agents for bacteriophage therapy due to a broad host range and high killing activity against clinical isolates. This work improves the current understanding of the phage infection physiology by transcriptome analysis. The expression profiles of a typical member of the Kayvirus genus (vB_SauM-515A1) were obtained at three time-points post-infection using RNA sequencing. A total of 35 transcription units comprising 238 ORFs were established. The sequences for 58 early and 12 late promoters were identified in the phage genome. The early promoters represent the strong sigma-70 promoters consensus sequence and control the host-dependent expression of 26 transcription units (81% of genes). The late promoters exclusively controlled the expression of four transcription units, while the transcription of the other five units was directed by both types of promoters. The characteristic features of late promoters were long -10 box of TGTTATATTA consensus sequence and the absence of -35 boxes. The data obtained are also of general interest, demonstrating a strategy of the phage genome expression with a broad overlap of the early and late transcription phases without any middle transcription, which is unusual for the large phage genomes (>100 kbp). Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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19 pages, 7380 KiB

Open AccessArticle

Wine Phenolic Compounds Differently Affect the Host-Killing Activity of Two Lytic Bacteriophages Infecting the Lactic Acid Bacterium Oenococcus oeni

by Cécile Philippe, Amel Chaïb, Fety Jaomanjaka, Stéphanie Cluzet, Aurélie Lagarde, Patricia Ballestra, Alain Decendit, Mélina Petrel, Olivier Claisse, Adeline Goulet, Christian Cambillau and Claire Le Marrec

Viruses 2020, 12(11), 1316; https://doi.org/10.3390/v12111316 - 17 Nov 2020

Cited by 11 | Viewed by 3208

Abstract

To provide insights into phage-host interactions during winemaking, we assessed whether phenolic compounds modulate the phage predation of Oenococcus oeni. Centrifugal partition chromatography was used to fractionate the phenolic compounds of a model red wine. The ability of lytic oenophage OE33PA to kill its host was reduced in the presence of two collected fractions in which we identified five compounds. Three, namely, quercetin, myricetin and p-coumaric acid, significantly reduced the phage predation of O. oeni when provided as individual pure molecules, as also did other structurally related compounds such as cinnamic acid. Their presence was correlated with a reduced adsorption rate of phage OE33PA on its host. Strikingly, none of the identified compounds affected the killing activity of the distantly related lytic phage Vinitor162. OE33PA and Vinitor162 were shown to exhibit different entry mechanisms to penetrate into bacterial cells. We propose that ligand-receptor interactions that mediate phage adsorption to the cell surface are diverse in O. oeni and are subject to differential interference by phenolic compounds. Their presence did not induce any modifications in the cell surface as visualized by TEM. Interestingly, docking analyses suggest that quercetin and cinnamic acid may interact with the tail of OE33PA and compete with host recognition. Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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10 pages, 2575 KiB

Open AccessArticle

VIRIDIC—A Novel Tool to Calculate the Intergenomic Similarities of Prokaryote-Infecting Viruses

by Cristina Moraru, Arvind Varsani and Andrew M. Kropinski

Viruses 2020, 12(11), 1268; https://doi.org/10.3390/v12111268 - 6 Nov 2020

Cited by 361 | Viewed by 13069

Abstract

Nucleotide-based intergenomic similarities are useful to understand how viruses are related with each other and to classify them. Here we have developed VIRIDIC, which implements the traditional algorithm used by the International Committee on Taxonomy of Viruses (ICTV), Bacterial and Archaeal Viruses Subcommittee, to calculate virus intergenomic similarities. When compared with other software, VIRIDIC gave the best agreement with the traditional algorithm, which is based on the percent identity between two genomes determined by BLASTN. Furthermore, VIRIDIC proved best at estimating the relatedness between more distantly-related phages, relatedness that other tools can significantly overestimate. In addition to the intergenomic similarities, VIRIDIC also calculates three indicators of the alignment ability to capture the relatedness between viruses: the aligned fractions for each genome in a pair and the length ratio between the two genomes. The main output of VIRIDIC is a heatmap integrating the intergenomic similarity values with information regarding the genome lengths and the aligned genome fraction. Additionally, VIRIDIC can group viruses into clusters, based on user-defined intergenomic similarity thresholds. The sensitivity of VIRIDIC is given by the BLASTN. Thus, it is able to capture relationships between viruses having in common even short genomic regions, with as low as 65% similarity. Below this similarity level, protein-based analyses should be used, as they are the best suited to capture distant relationships. VIRIDIC is available at viridic.icbm.de, both as a web-service and a stand-alone tool. It allows fast analysis of large phage genome datasets, especially in the stand-alone version, which can be run on the user’s own servers and can be integrated in bioinformatics pipelines. VIRIDIC was developed having viruses of Bacteria and Archaea in mind; however, it could potentially be used for eukaryotic viruses as well, as long as they are monopartite. Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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23 pages, 7351 KiB

Open AccessArticle

Exploring the Remarkable Diversity of Culturable Escherichia coli Phages in the Danish Wastewater Environment

by Nikoline S. Olsen, Laura Forero-Junco, Witold Kot and Lars H. Hansen

Viruses 2020, 12(9), 986; https://doi.org/10.3390/v12090986 - 4 Sep 2020

Cited by 31 | Viewed by 5218

Abstract

Phages drive bacterial diversity, profoundly influencing microbial communities, from microbiomes to the drivers of global biogeochemical cycling. Aiming to broaden our understanding of Escherichia coli (MG1655, K-12) phages, we screened 188 Danish wastewater samples and isolated 136 phages. Ninety-two of these have genomic sequences with less than 95% similarity to known phages, while most map to existing genera several represent novel lineages. The isolated phages are highly diverse, estimated to represent roughly one-third of the true diversity of culturable virulent dsDNA Escherichia phages in Danish wastewater, yet almost half (40%) are not represented in metagenomic databases, emphasising the importance of isolating phages to uncover diversity. Seven viral families, Myoviridae, Siphoviridae, Podoviridae, Drexlerviridae, Chaseviridae, Autographviridae, and Microviridae, are represented in the dataset. Their genomes vary drastically in length from 5.3 kb to 170.8 kb, with a guanine and cytosine (GC) content ranging from 35.3% to 60.0%. Hence, even for a model host bacterium, substantial diversity remains to be uncovered. These results expand and underline the range of coliphage diversity and demonstrate how far we are from fully disclosing phage diversity and ecology. Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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18 pages, 4952 KiB

Open AccessArticle

The Phage-Encoded N-Acetyltransferase Rac Mediates Inactivation of Pseudomonas aeruginosa Transcription by Cleavage of the RNA Polymerase Alpha Subunit

by Pieter-Jan Ceyssens, Jeroen De Smet, Jeroen Wagemans, Natalia Akulenko, Evgeny Klimuk, Subray Hedge, Marleen Voet, Hanne Hendrix, Jan Paeshuyse, Bart Landuyt, Hua Xu, John Blanchard, Konstantin Severinov and Rob Lavigne

Viruses 2020, 12(9), 976; https://doi.org/10.3390/v12090976 - 2 Sep 2020

Cited by 11 | Viewed by 4486

Abstract

In this study, we describe the biological function of the phage-encoded protein RNA polymerase alpha subunit cleavage protein (Rac), a predicted Gcn5-related acetyltransferase encoded by phiKMV-like viruses. These phages encode a single-subunit RNA polymerase for transcription of their late (structure- and lysis-associated) genes, whereas the bacterial RNA polymerase is used at the earlier stages of infection. Rac mediates the inactivation of bacterial transcription by introducing a specific cleavage in the α subunit of the bacterial RNA polymerase. This cleavage occurs within the flexible linker sequence and disconnects the C-terminal domain, required for transcription initiation from most highly active cellular promoters. To achieve this, Rac likely taps into a novel post-translational modification (PTM) mechanism within the host Pseudomonas aeruginosa. From an evolutionary perspective, this novel phage-encoded regulation mechanism confirms the importance of PTMs in the prokaryotic metabolism and represents a new way by which phages can hijack the bacterial host metabolism. Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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16 pages, 3437 KiB

Open AccessArticle

Novel Escherichia coli RNA Polymerase Binding Protein Encoded by Bacteriophage T5

by Evgeny Klimuk, Vladimir Mekler, Darya Lavysh, Marina Serebryakova, Natalia Akulenko and Konstantin Severinov

Viruses 2020, 12(8), 807; https://doi.org/10.3390/v12080807 - 26 Jul 2020

Cited by 7 | Viewed by 3709

Abstract

The Escherichia coli bacteriophage T5 has three temporal classes of genes (pre-early, early, and late). All three classes are transcribed by host RNA polymerase (RNAP) containing the σ⁷⁰ promoter specificity subunit. Molecular mechanisms responsible for the switching of viral transcription from one class to another remain unknown. Here, we find the product of T5 gene 026 (gpT5.026) in RNAP preparations purified from T5-infected cells and demonstrate in vitro its tight binding to E. coli RNAP. While proteins homologous to gpT5.026 are encoded by all T5-related phages, no similarities to proteins with known functions can be detected. GpT5.026 binds to two regions of the RNAP β subunit and moderately inhibits RNAP interaction with the discriminator region of σ⁷⁰-dependent promoters. A T5 mutant with disrupted gene 026 is viable, but the host cell lysis phase is prolongated and fewer virus particles are produced. During the mutant phage infection, the number of early transcripts increases, whereas the number of late transcripts decreases. We propose that gpT5.026 is part of the regulatory cascade that orchestrates a switch from early to late bacteriophage T5 transcription. Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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13 pages, 3739 KiB

Open AccessArticle

A Lactococcal Phage Protein Promotes Viral Propagation and Alters the Host Proteomic Response During Infection

by Marie-Laurence Lemay, Sandra Maaß, Andreas Otto, Jérémie Hamel, Pier-Luc Plante, Geneviève M. Rousseau, Denise M. Tremblay, Rong Shi, Jacques Corbeil, Stéphane M. Gagné, Dörte Becher and Sylvain Moineau

Viruses 2020, 12(8), 797; https://doi.org/10.3390/v12080797 - 24 Jul 2020

Cited by 4 | Viewed by 3248

Abstract

The lactococcal virulent phage p2 is a model for studying the Skunavirus genus, the most prevalent group of phages causing milk fermentation failures in cheese factories worldwide. This siphophage infects Lactococcus lactis MG1363, a model strain used to study Gram-positive lactic acid bacteria. The structural proteins of phage p2 have been thoroughly described, while most of its non-structural proteins remain uncharacterized. Here, we developed an integrative approach, making use of structural biology, genomics, physiology, and proteomics to provide insights into the function of ORF47, the most conserved non-structural protein of unknown function among the Skunavirus genus. This small phage protein, which is composed of three α-helices, was found to have a major impact on the bacterial proteome during phage infection and to significantly reduce the emergence of bacteriophage-insensitive mutants. Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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Review

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21 pages, 1308 KiB

Open AccessReview

RNA Viruses in Aquatic Unicellular Eukaryotes

by Mohammadreza Sadeghi, Yuji Tomaru and Tero Ahola

Viruses 2021, 13(3), 362; https://doi.org/10.3390/v13030362 - 25 Feb 2021

Cited by 20 | Viewed by 6540

Abstract

Increasing sequence information indicates that RNA viruses constitute a major fraction of marine virus assemblages. However, only 12 RNA virus species have been described, infecting known host species of marine single-celled eukaryotes. Eight of these use diatoms as hosts, while four are resident in dinoflagellate, raphidophyte, thraustochytrid, or prasinophyte species. Most of these belong to the order Picornavirales, while two are divergent and fall into the families Alvernaviridae and Reoviridae. However, a very recent study has suggested that there is extraordinary diversity in aquatic RNA viromes, describing thousands of viruses, many of which likely use protist hosts. Thus, RNA viruses are expected to play a major ecological role for marine unicellular eukaryotic hosts. In this review, we describe in detail what has to date been discovered concerning viruses with RNA genomes that infect aquatic unicellular eukaryotes. Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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15 pages, 2277 KiB

Open AccessReview

Viral Hijack of Filamentous Surface Structures in Archaea and Bacteria

by Colin Tittes, Sabine Schwarzer and Tessa E. F. Quax

Viruses 2021, 13(2), 164; https://doi.org/10.3390/v13020164 - 22 Jan 2021

Cited by 15 | Viewed by 3614

Abstract

The bacterial and archaeal cell surface is decorated with filamentous surface structures that are used for different functions, such as motility, DNA exchange and biofilm formation. Viruses hijack these structures and use them to ride to the cell surface for successful entry. In this review, we describe currently known mechanisms for viral attachment, translocation, and entry via filamentous surface structures. We describe the different mechanisms used to exploit various surface structures bacterial and archaeal viruses. This overview highlights the importance of filamentous structures at the cell surface for entry of prokaryotic viruses. Full article

(This article belongs to the Special Issue Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes)

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Viruses of Microbes 2020: The Latest Conquests on Viruses of Microbes

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