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DNA Packaging Dynamics of Bacteriophages
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DNA Packaging Dynamics of Bacteriophages

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: closed (31 December 2022) | Viewed by 5361

Special Issue Editor

Prof. Dr. Philip Serwer

E-Mail Website
Guest Editor
Department of Biochemistry and Structural Biology, University of Texas Health Center, San Antonio, TX, USA
Interests: phage assembly; phage-derived biotherapeutics; phage genomics; nanoparticle fractionation

Special Issue Information

Dear Colleagues,

This special issue will focus primarily on gaps in published studies of the DNA packaging of double-stranded DNA bacteriophages. Articles with any of three foci are of interest: (1) use of theory, including molecular dynamics simulation, to either fill or move significantly toward filling a known, unfilled gap, (2) novel experiments that produce data for the filling a known, unfilled gap, (3) identification of gaps that are not sufficiently (or not at all) expressed in the literature. A secondary focus is the use of basic studies of bacteriophage DNA packaging and bacteriophage structure to fill biomedical gaps (e.g., T4 fibritin message in RNA vaccines). Historically, the Caltech phage laboratory was funded, in part, by the National Foundation (i.e., the March of Dimes), known for its “seeing around a biomedical corner” in the case of the Salk and Sabin polio vaccines. Maybe, it saw around more than one.

Pure clinical studies are out of scope of the Special Issue, however, clinical submissions with biomolecular experiments are welcome.

Prof. Dr. Philip Serwer
Guest Editor

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. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. 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

  • Bacteriophage
  • Biomedical Gaps
  • DNA dynamics
  • DNA Biochemistry
  • High-Resolution Structure
  • Macromolecular Assembly
  • Molecular Dynamics Simulation
  • Single-molecule Analysis

Published Papers (3 papers)

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Research

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21 pages, 3982 KiB  
Article
Siphophage 0105phi7-2 of Bacillus thuringiensis: Novel Propagation, DNA, and Genome-Implied Assembly
by Samantha M. Roberts, Miranda Aldis, Elena T. Wright, Cara B. Gonzales, Zhao Lai, Susan T. Weintraub, Stephen C. Hardies and Philip Serwer
Int. J. Mol. Sci. 2023, 24(10), 8941; https://doi.org/10.3390/ijms24108941 - 18 May 2023
Cited by 3 | Viewed by 1386
Abstract
Diversity of phage propagation, physical properties, and assembly promotes the use of phages in ecological studies and biomedicine. However, observed phage diversity is incomplete. Bacillus thuringiensis siphophage, 0105phi-7-2, first described here, significantly expands known phage diversity, as seen via in-plaque propagation, electron microscopy, [...] Read more.
Diversity of phage propagation, physical properties, and assembly promotes the use of phages in ecological studies and biomedicine. However, observed phage diversity is incomplete. Bacillus thuringiensis siphophage, 0105phi-7-2, first described here, significantly expands known phage diversity, as seen via in-plaque propagation, electron microscopy, whole genome sequencing/annotation, protein mass spectrometry, and native gel electrophoresis (AGE). Average plaque diameter vs. plaque-supporting agarose gel concentration plots reveal unusually steep conversion to large plaques as agarose concentration decreases below 0.2%. These large plaques sometimes have small satellites and are made larger by orthovanadate, an ATPase inhibitor. Phage head–host-cell binding is observed by electron microscopy. We hypothesize that this binding causes plaque size-increase via biofilm evolved, ATP stimulated ride-hitching on motile host cells by temporarily inactive phages. Phage 0105phi7-2 does not propagate in liquid culture. Genomic sequencing/annotation reveals history as temperate phage and distant similarity, in a virion-assembly gene cluster, to prototypical siphophage SPP1 of Bacillus subtilis. Phage 0105phi7-2 is distinct in (1) absence of head-assembly scaffolding via either separate protein or classically sized, head protein-embedded peptide, (2) producing partially condensed, head-expelled DNA, and (3) having a surface relatively poor in AGE-detected net negative charges, which is possibly correlated with observed low murine blood persistence. Full article
(This article belongs to the Special Issue DNA Packaging Dynamics of Bacteriophages)
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Review

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22 pages, 7512 KiB  
Review
RNA Packaging in the Cystovirus Bacteriophages: Dynamic Interactions during Capsid Maturation
by Paul Gottlieb and Aleksandra Alimova
Int. J. Mol. Sci. 2022, 23(5), 2677; https://doi.org/10.3390/ijms23052677 - 28 Feb 2022
Cited by 7 | Viewed by 2011
Abstract
The bacteriophage family Cystoviridae consists of a single genus, Cystovirus, that is lipid-containing with three double-stranded RNA (ds-RNA) genome segments. With regard to the segmented dsRNA genome, they resemble the family Reoviridae. Therefore, the Cystoviruses have long served as a simple [...] Read more.
The bacteriophage family Cystoviridae consists of a single genus, Cystovirus, that is lipid-containing with three double-stranded RNA (ds-RNA) genome segments. With regard to the segmented dsRNA genome, they resemble the family Reoviridae. Therefore, the Cystoviruses have long served as a simple model for reovirus assembly. This review focuses on important developments in the study of the RNA packaging and replication mechanisms, emphasizing the structural conformations and dynamic changes during maturation of the five proteins required for viral RNA synthesis, P1, P2, P4, P7, and P8. Together these proteins constitute the procapsid/polymerase complex (PC) and nucleocapsid (NC) of the Cystoviruses. During viral assembly and RNA packaging, the five proteins must function in a coordinated fashion as the PC and NC undergo expansion with significant position translation. The review emphasizes this facet of the viral assembly process and speculates on areas suggestive of additional research efforts. Full article
(This article belongs to the Special Issue DNA Packaging Dynamics of Bacteriophages)
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Other

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8 pages, 482 KiB  
Perspective
A Perspective on Studies of Phage DNA Packaging Dynamics
by Philip Serwer
Int. J. Mol. Sci. 2022, 23(14), 7854; https://doi.org/10.3390/ijms23147854 - 16 Jul 2022
Viewed by 1425
Abstract
The Special Issue “DNA Packaging Dynamics of Bacteriophages” is focused on an event that is among the physically simplest known events with biological character. Thus, phage DNA (and RNA) packaging is used as a relatively accessible model for physical analysis of all biological [...] Read more.
The Special Issue “DNA Packaging Dynamics of Bacteriophages” is focused on an event that is among the physically simplest known events with biological character. Thus, phage DNA (and RNA) packaging is used as a relatively accessible model for physical analysis of all biological events. A similar perspective motivated early phage-directed work, which was a major contributor to early molecular biology. However, analysis of DNA packaging encounters the limitation that phages vary in difficulty of observing various aspects of their packaging. If a difficult-to-access aspect arises while using a well-studied phage, a counterstrategy is to (1) look for and use phages that provide a better access “window” and (2) integrate multi-phage-accessed information with the help of chemistry and physics. The assumption is that all phages are characterized by the same evolution-derived themes, although with variations. Universal principles will emerge from the themes. A spin-off of using this strategy is the isolation and characterization of the diverse phages needed for biomedicine. Below, I give examples in the areas of infectious disease, cancer, and neurodegenerative disease. Full article
(This article belongs to the Special Issue DNA Packaging Dynamics of Bacteriophages)
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