Genetics and Genomics in Bacteriophage-Host Interactions

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Microbial Genetics and Genomics".

Deadline for manuscript submissions: closed (25 November 2023) | Viewed by 4661

Special Issue Editors

Yunnan Institute of Microbiology, Yunnan University, Kunming 650091, China
Interests: bacteriophage-host interaction; virome; bacteriophage therapy; aquatic viral ecology; halovirus
1. Joint Laboratory of Microbial Oceanography, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China
2. University of Chinese Academy of Sciences, Beijing, China
Interests: viromics; algae-bacteria-phage interactions; aquatic viral ecology; phage therapy; microbially driven carbon cycle
Special Issues, Collections and Topics in MDPI journals
Shenzhen Institute of Respiratory Diseases, The First Affiliated Hospital (Shenzhen People's Hospital), Shenzhen 518003, China
Interests: bacteriophage resistance; antibiotic resistance; bacterial–host interactions; bacterial pathogenesis

Special Issue Information

Dear Colleagues,

This Special Issue is intended to give new insights to underlying mechanisms of bacteriophage–host interactions, as well as to promote the understanding of the ecological function of bacteriophages and the development of bacteriophage applications. Bacteriophages play important roles in disseminating antibiotic resistance genes and virulence genes through horizontal gene transfer and can expand the niche adaptation and competitive advantages of hosts. Bacteriophages can also improve host stress resistance and metabolism by expressing auxiliary metabolic genes. Bacteriophages drive host phenotypic and genotypic variations through lysogens and/or coevolution. This Special Issue focus on studies that use genetic and (meta)genomic technologies to explore interactions between bacteriophages and hosts on multiple levels (communities or single cells).

Dr. Wei Xiao
Prof. Dr. Yongyu Zhang
Dr. Kai Zhou
Guest Editors

Manuscript Submission Information

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Keywords

  • bacteriophage
  • virome
  • phageome
  • phage–host interaction
  • bioinformatics
  • temperate phages
  • phage therapy
  • auxiliary metabolic genes

Published Papers (3 papers)

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Research

35 pages, 12340 KiB  
Article
Molecular Characterization and Genome Mechanical Features of Two Newly Isolated Polyvalent Bacteriophages Infecting Pseudomonas syringae pv. garcae
by Erica C. Silva, Carlos A. Quinde, Basilio Cieza, Aakash Basu, Marta M. D. C. Vila and Victor M. Balcão
Genes 2024, 15(1), 113; https://doi.org/10.3390/genes15010113 - 18 Jan 2024
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Abstract
Coffee plants have been targeted by a devastating bacterial disease, a condition known as bacterial blight, caused by the phytopathogen Pseudomonas syringae pv. garcae (Psg). Conventional treatments of coffee plantations affected by the disease involve frequent spraying with copper- and kasugamycin-derived compounds, but [...] Read more.
Coffee plants have been targeted by a devastating bacterial disease, a condition known as bacterial blight, caused by the phytopathogen Pseudomonas syringae pv. garcae (Psg). Conventional treatments of coffee plantations affected by the disease involve frequent spraying with copper- and kasugamycin-derived compounds, but they are both highly toxic to the environment and stimulate the appearance of bacterial resistance. Herein, we report the molecular characterization and mechanical features of the genome of two newly isolated (putative polyvalent) lytic phages for Psg. The isolated phages belong to class Caudoviricetes and present a myovirus-like morphotype belonging to the genuses Tequatrovirus (PsgM02F) and Phapecoctavirus (PsgM04F) of the subfamilies Straboviridae (PsgM02F) and Stephanstirmvirinae (PsgM04F), according to recent bacterial viruses’ taxonomy, based on their complete genome sequences. The 165,282 bp (PsgM02F) and 151,205 bp (PsgM04F) genomes do not feature any lysogenic-related (integrase) genes and, hence, can safely be assumed to follow a lytic lifestyle. While phage PsgM02F produced a morphogenesis yield of 124 virions per host cell, phage PsgM04F produced only 12 virions per host cell, indicating that they replicate well in Psg with a 50 min latency period. Genome mechanical analyses established a relationship between genome bendability and virion morphogenesis yield within infected host cells. Full article
(This article belongs to the Special Issue Genetics and Genomics in Bacteriophage-Host Interactions)
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16 pages, 3721 KiB  
Article
Extracellular Polysaccharide Receptor and Receptor-Binding Proteins of the Rhodobacter capsulatus Bacteriophage-like Gene Transfer Agent RcGTA
by Nawshin T. B. Alim, Sonja Koppenhöfer, Andrew S. Lang and J. Thomas Beatty
Genes 2023, 14(5), 1124; https://doi.org/10.3390/genes14051124 - 22 May 2023
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Abstract
A variety of prokaryotes produce a bacteriophage-like gene transfer agent (GTA), and the alphaproteobacterial Rhodobacter capsulatus RcGTA is a model GTA. Some environmental isolates of R. capsulatus lack the ability to acquire genes transferred by the RcGTA (recipient capability). In this work, we [...] Read more.
A variety of prokaryotes produce a bacteriophage-like gene transfer agent (GTA), and the alphaproteobacterial Rhodobacter capsulatus RcGTA is a model GTA. Some environmental isolates of R. capsulatus lack the ability to acquire genes transferred by the RcGTA (recipient capability). In this work, we investigated the reason why R. capsulatus strain 37b4 lacks recipient capability. The RcGTA head spike fiber and tail fiber proteins have been proposed to bind extracellular oligosaccharide receptors, and strain 37b4 lacks a capsular polysaccharide (CPS). The reason why strain 37b4 lacks a CPS was unknown, as was whether the provision of a CPS to 37b4 would result in recipient capability. To address these questions, we sequenced and annotated the strain 37b4 genome and used BLAST interrogations of this genome sequence to search for homologs of genes known to be needed for R. capsulatus recipient capability. We also created a cosmid-borne genome library from a wild-type strain, mobilized the library into 37b4, and used the cosmid-complemented strain 37b4 to identify genes needed for a gain of function, allowing for the acquisition of RcGTA-borne genes. The relative presence of CPS around a wild-type strain, 37b4, and cosmid-complemented 37b4 cells was visualized using light microscopy of stained cells. Fluorescently tagged head spike fiber and tail fiber proteins of the RcGTA particle were created and used to measure the relative binding to wild-type and 37b4 cells. We found that strain 37b4 lacks recipient capability because of an inability to bind RcGTA; the reason it is incapable of binding is that it lacks CPS, and the absence of CPS is due to the absence of genes previously shown to be needed for CPS production in another strain. In addition to the head spike fiber, we found that the tail fiber protein also binds to the CPS. Full article
(This article belongs to the Special Issue Genetics and Genomics in Bacteriophage-Host Interactions)
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12 pages, 1729 KiB  
Article
DNA Gyrase Inhibitors Increase the Frequency of Bacteriophage-like RcGTA-Mediated Gene Transfer in Rhodobacter capsulatus
by Rachel Bernelot-Moens and J. Thomas Beatty
Genes 2022, 13(11), 2071; https://doi.org/10.3390/genes13112071 - 09 Nov 2022
Cited by 1 | Viewed by 1657
Abstract
Rhodobacter capsulatus produces a bacteriophage-like particle called the gene transfer agent (RcGTA) that mediates horizontal gene transfer. RcGTA particles transfer random ~4.5-kb fragments of genomic DNA that integrate into recipient genomes by allelic replacement. This work addresses the effect of sub-inhibitory concentrations of [...] Read more.
Rhodobacter capsulatus produces a bacteriophage-like particle called the gene transfer agent (RcGTA) that mediates horizontal gene transfer. RcGTA particles transfer random ~4.5-kb fragments of genomic DNA that integrate into recipient genomes by allelic replacement. This work addresses the effect of sub-inhibitory concentrations of antibiotics on gene transfer by RcGTA. A transduction assay was developed to test the effects of various substances on gene transfer. Using this assay, low concentrations of DNA gyrase inhibitors were found to increase the frequency of gene transfer. Novobiocin was studied in more detail, and it was found that this antibiotic did not influence the production or release of RcGTA but instead appeared to act on the recipient cells. The target of novobiocin in other species has been shown to be the GyrB subunit of DNA gyrase (a heterotetramer of 2GyrA and 2GyrB). R. capsulatus encodes GyrA and GyrB homologues, and a GyrB overexpression plasmid was created and found to confer resistance to novobiocin. The presence of the overexpression plasmid in recipient cells greatly diminished the novobiocin-mediated increase in gene transfer, confirming that this effect is due to the binding of novobiocin by GyrB. The results of this work show that antibiotics affect gene transfer in R. capsulatus and may be relevant to microbial genetic exchange in natural ecosystems. Full article
(This article belongs to the Special Issue Genetics and Genomics in Bacteriophage-Host Interactions)
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