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Viruses
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Phage Assembly Pathways — to the Memory of Lindsay Black 2.0
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Phage Assembly Pathways — to the Memory of Lindsay Black 2.0

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

Deadline for manuscript submissions: 30 June 2024 | Viewed by 3223

Special Issue Editors

Prof. Dr. Andreas Kuhn

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Guest Editor
Institute of Microbiology and Molecular Biology, University of Hohenheim, Stuttgart, Germany
Interests: filamentous phages; protein
Special Issues, Collections and Topics in MDPI journals
Dr. Julie Thomas

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Guest Editor
Thomas H. Gosnell School of Life Sciences, College of Science, Rochester Institute of Technology, Rochester, NY, USA
Interests: giant phages; phage structure/assembly; genomics; genetics; proteomics; host–phage interactions
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Most fascinating in protein biochemistry are the complex assembly systems that we know from phage and virus particles. Phage assembly occurs within the prokaryotic host cell and involves replicated genetic material and viral proteins being transformed into infectious progeny. The assembly of each bacteriophage particle results from a self-triggered process that is exquisitely controlled by a series of conformational cascades. In general, each assembly process is initiated by an oligomeric protein that recruits defined partner proteins in consecutive steps creating an assembly product of increasing complexity. The driving mechanism for this process is hidden in the intrinsic conformational flexibility of each protein which drives the assembly reaction forward. Therefore, numbers of phage assembly steps have been able to be reconstituted in vitro without any energetic input from the host.

Much of what we currently know regarding phage assembly is derived from the study of the classic phage systems, such as that of T4. Yet, even for such model systems there remain major unresolved questions. In addition, for the many of the more recently discovered phages, there is a myriad of questions regarding how their virions assemble. To address these questions an impressive array of experimental approaches is now available. These include the recent advent of novel technologies such as high-resolution tomography and cryo-electron microscopy which when combined with biochemical methods allow us to follow these processes in molecular detail and possibly even at an atomic resolution.

This special issue is dedicated to Lindsay W. Black. Lindsay was a great leader in the field of phage assembly. Sadly, Lindsay passed away early 2021. For over 40 years, Lindsay dissected the molecular processes by which the T4 head assembles in his laboratory at the University of Maryland. Using the T4 system, Lindsay became a central figure in the field of DNA packaging and he continued to make contributions to this field for most of his career. Lindsay was also fascinated by other aspects of phage assembly and replication and made significant contributions to various other areas, including virus structure, and prohead assembly and maturation. Lindsay was a brilliant scientist and a true friend to many. To honor Lindsay’s legacy, we welcome submissions to this special issue that focuses on Lindsay’s research passion, phage assembly.

Prof. Dr. Andreas Kuhn
Dr. Julie Thomas
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

  • capsid assembly
  • DNA packaging
  • portal assembly
  • host receptor
  • tail contraction
  • ejectosome assembly
  • DNA translocation
  • lysis control

Published Papers (4 papers)

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Research

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18 pages, 2642 KiB  
Article
Lysis Physiology of Pseudomonas aeruginosa Infected with ssRNA Phage PRR1
by Rimantas Daugelavičius, Greta Daujotaitė and Dennis H. Bamford
Viruses 2024, 16(4), 645; https://doi.org/10.3390/v16040645 - 21 Apr 2024
Viewed by 449
Abstract
The phage PRR1 belongs to the Leviviridae family, a group of ssRNA bacteriophages that infect Gram-negative bacteria. The variety of host cells is determined by the specificity of PRR1 to a pilus encoded by a broad host range of IncP-type plasmids that confer [...] Read more.
The phage PRR1 belongs to the Leviviridae family, a group of ssRNA bacteriophages that infect Gram-negative bacteria. The variety of host cells is determined by the specificity of PRR1 to a pilus encoded by a broad host range of IncP-type plasmids that confer multiple types of antibiotic resistance to the host. Using P. aeruginosa strain PAO1 as a host, we analyzed the PRR1 infection cycle, focusing on cell lysis. PRR1 infection renders P. aeruginosa cells sensitive to lysozyme approximately 20 min before the start of a drop in suspension turbidity. At the same time, infected cells start to accumulate lipophilic anions. The on-line monitoring of the entire infection cycle showed that single-gene-mediated lysis strongly depends on the host cells’ physiological state. The blockage of respiration or a reduction in the intracellular ATP concentration during the infection resulted in the inhibition of lysis. The same effect was observed when the synthesis of PRR1 lysis protein was induced in an E. coli expression system. In addition, lysis was strongly dependent on the level of aeration. Dissolved oxygen concentrations sufficient to support cell growth did not ensure efficient lysis, and a coupling between cell lysis initiation and aeration level was observed. However, the duration of the drop in suspension turbidity did not depend on the level of aeration. Full article
(This article belongs to the Special Issue Phage Assembly Pathways — to the Memory of Lindsay Black 2.0)
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13 pages, 6826 KiB  
Article
Involvement of the Cell Division Protein DamX in the Infection Process of Bacteriophage T4
by Sabrina Wenzel, Renate Hess, Dorothee Kiefer and Andreas Kuhn
Viruses 2024, 16(4), 487; https://doi.org/10.3390/v16040487 - 22 Mar 2024
Viewed by 590
Abstract
The molecular mechanism of how the infecting DNA of bacteriophage T4 passes from the capsid through the bacterial cell wall and enters the cytoplasm is essentially unknown. After adsorption, the short tail fibers of the infecting phage extend from the baseplate and trigger [...] Read more.
The molecular mechanism of how the infecting DNA of bacteriophage T4 passes from the capsid through the bacterial cell wall and enters the cytoplasm is essentially unknown. After adsorption, the short tail fibers of the infecting phage extend from the baseplate and trigger the contraction of the tail sheath, leading to a puncturing of the outer membrane by the tail tip needle composed of the proteins gp5.4, gp5 and gp27. To explore the events that occur in the periplasm and at the inner membrane, we constructed T4 phages that have a modified gp27 in their tail tip with a His-tag. Shortly after infection with these phages, cells were chemically cross-linked and solubilized. The cross-linked products were affinity-purified on a nickel column and the co-purified proteins were identified by mass spectrometry, and we found that predominantly the inner membrane proteins DamX, SdhA and PpiD were cross-linked. The same partner proteins were identified when purified gp27 was added to Escherichia coli spheroplasts, suggesting a direct protein–protein interaction. Full article
(This article belongs to the Special Issue Phage Assembly Pathways — to the Memory of Lindsay Black 2.0)
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23 pages, 7612 KiB  
Article
Genomic and Proteomic Analysis of Six Vi01-like Phages Reveals Wide Host Range and Multiple Tail Spike Proteins
by Evan B. Harris, Kenneth K. K. Ewool, Lucy C. Bowden, Jonatan Fierro, Daniel Johnson, McKay Meinzer, Sadie Tayler and Julianne H. Grose
Viruses 2024, 16(2), 289; https://doi.org/10.3390/v16020289 - 13 Feb 2024
Viewed by 840
Abstract
Enterobacteriaceae is a large family of Gram-negative bacteria composed of many pathogens, including Salmonella and Shigella. Here, we characterize six bacteriophages that infect Enterobacteriaceae, which were isolated from wastewater plants in the Wasatch front (Utah, United States). These phages are highly similar [...] Read more.
Enterobacteriaceae is a large family of Gram-negative bacteria composed of many pathogens, including Salmonella and Shigella. Here, we characterize six bacteriophages that infect Enterobacteriaceae, which were isolated from wastewater plants in the Wasatch front (Utah, United States). These phages are highly similar to the Kuttervirus vB_SenM_Vi01 (Vi01), which was isolated using wastewater from Kiel, Germany. The phages vary little in genome size and are between 157 kb and 164 kb, which is consistent with the sizes of other phages in the Vi01-like phage family. These six phages were characterized through genomic and proteomic comparison, mass spectrometry, and both laboratory and clinical host range studies. While their proteomes are largely unstudied, mass spectrometry analysis confirmed the production of five hypothetical proteins, several of which unveiled a potential operon that suggests a ferritin-mediated entry system on the Vi01-like phage family tail. However, no dependence on this pathway was observed for the single host tested herein. While unable to infect every genus of Enterobacteriaceae tested, these phages are extraordinarily broad ranged, with several demonstrating the ability to infect Salmonella enterica and Citrobacter freundii strains with generally high efficiency, as well as several clinical Salmonella enterica isolates, most likely due to their multiple tail fibers. Full article
(This article belongs to the Special Issue Phage Assembly Pathways — to the Memory of Lindsay Black 2.0)
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Review

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21 pages, 4199 KiB  
Review
Mechanism of Viral DNA Packaging in Phage T4 Using Single-Molecule Fluorescence Approaches
by Souradip Dasgupta, Julie A. Thomas and Krishanu Ray
Viruses 2024, 16(2), 192; https://doi.org/10.3390/v16020192 - 26 Jan 2024
Viewed by 951
Abstract
In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the [...] Read more.
In all tailed phages, the packaging of the double-stranded genome into the head by a terminase motor complex is an essential step in virion formation. Despite extensive research, there are still major gaps in the understanding of this highly dynamic process and the mechanisms responsible for DNA translocation. Over the last fifteen years, single-molecule fluorescence technologies have been applied to study viral nucleic acid packaging using the robust and flexible T4 in vitro packaging system in conjunction with genetic, biochemical, and structural analyses. In this review, we discuss the novel findings from these studies, including that the T4 genome was determined to be packaged as an elongated loop via the colocalization of dye-labeled DNA termini above the portal structure. Packaging efficiency of the TerL motor was shown to be inherently linked to substrate structure, with packaging stalling at DNA branches. The latter led to the design of multiple experiments whose results all support a proposed torsional compression translocation model to explain substrate packaging. Evidence of substrate compression was derived from FRET and/or smFRET measurements of stalled versus resolvase released dye-labeled Y-DNAs and other dye-labeled substrates relative to motor components. Additionally, active in vivo T4 TerS fluorescent fusion proteins facilitated the application of advanced super-resolution optical microscopy toward the visualization of the initiation of packaging. The formation of twin TerS ring complexes, each expected to be ~15 nm in diameter, supports a double protein ring–DNA synapsis model for the control of packaging initiation, a model that may help explain the variety of ring structures reported among pac site phages. The examination of the dynamics of the T4 packaging motor at the single-molecule level in these studies demonstrates the value of state-of-the-art fluorescent tools for future studies of complex viral replication mechanisms. Full article
(This article belongs to the Special Issue Phage Assembly Pathways — to the Memory of Lindsay Black 2.0)
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