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Bacteriophage: Molecular Ecology and Pharmacology, 2nd Edition

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

Deadline for manuscript submissions: closed (31 October 2024) | Viewed by 844

Special Issue Editors


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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 Issues, Collections and Topics in MDPI journals

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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

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Guest Editor
1. North Carolina Research Campus (NCRC), Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Kannapolis, NC 28081, USA
2. Computational Intelligence to Predict Health and Environmental Risks (CIPHER) Research Center, Department of Bioinformatics and Genomics, The University of North Carolina at Charlotte, Charlotte, NC 28223, USA
Interests: multiomics; next generation sequencing; mass spectrometry; virology; de novo assembly; novel antivirals and antibiotics; bacteriophage therapy

Special Issue Information

Dear Colleagues,

The discovery of bacterial viruses (bacteriophages) in 1915 and 1917 by Frederick Twort and Felix d’Herelle respectively, resulted from the research projects that shared in modern terms both ecological and applied goals. During the decades of research that followed this seminal discovery, the attention of phage research shifted to general biology of phages though the applied aspect also remained. The ecological perspective almost vanished and returned to the stage only at the very end of XX century.

Nowadays it became clear that bacteriophages are one of the major forces that moves and shapes the fascinating landscape of microbial world and its interactions with the rest of the Biosphere population. Phages influence almost any known aspect of bacterial biology and adopt immense variety of strategies to exert their ‘hidden power’, ranging from direct killing of the bacterial cells to protecting the host populations by actively subverting the immune reactions of macroorganisms. At the same time the growing world-wide crisis caused by the rapid spread of multidrug resistant bacterial pathogens greatly revived the interest of the scientific community to bacteriophage-mediated biocontrol technologies, at the first place to phage therapy but also to phage applications in agriculture, food industry and other fields aiming to reduce the use of antibiotics outside of medical facilities.

Thus, the need for the convergence of ecological and applied approaches in bacteriophage biology directly streams from the contemporary concepts in this field. The outcome of phage therapy or phage biocontrol interventions is always a result of ecological interactions between bacteria, viruses and environment (including that of human or animal body). And the possibilities and limitations of these technologies are largely defined by molecular mechanisms of phage-host and/or phage-macroorganisms interactions.

To this special issue we are aiming to attract high-level research and review papers concerning molecular aspects of bacteriophage ecology in the broad sense of the latter term. This will include the papers on bacteriophage genomics and metagenomics in free-living or symbiotic microbial systems, mechanisms of bacteriophage host range determination, influence of bacterial physiology on interactions with viruses and other ecologically relevant research topics. The papers regarding direct phage interactions with macroorganisms, including phage pharmacokinetics issues are specially welcome.

Prof. Dr. Philip Serwer
Dr. Julie Thomas
Dr. Richard Allen White III
Guest Editors

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Keywords

  • bacteriophage ecology
  • bacteriophage pharmacology
  • intercell communication of bacteria
  • phage-host interactions
  • phage-host recognition
  • phage receptors
  • phage therapy

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Published Papers (1 paper)

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Research

27 pages, 6135 KiB  
Article
Hot Spots of Site-Specific Integration into the Sinorhizobium meliloti Chromosome
by Maria E. Vladimirova, Marina L. Roumiantseva, Alla S. Saksaganskaia, Victoria S. Muntyan, Sergey P. Gaponov and Alessio Mengoni
Int. J. Mol. Sci. 2024, 25(19), 10421; https://doi.org/10.3390/ijms251910421 - 27 Sep 2024
Viewed by 645
Abstract
The diversity of phage-related sequences (PRSs) and their site-specific integration into the genomes of nonpathogenic, agriculturally valuable, nitrogen-fixing root nodule bacteria, such as Sinorhizobium meliloti, were evaluated in this study. A total of 314 PRSs, ranging in size from 3.24 kb to [...] Read more.
The diversity of phage-related sequences (PRSs) and their site-specific integration into the genomes of nonpathogenic, agriculturally valuable, nitrogen-fixing root nodule bacteria, such as Sinorhizobium meliloti, were evaluated in this study. A total of 314 PRSs, ranging in size from 3.24 kb to 88.98 kb, were identified in the genomes of 27 S. meliloti strains. The amount of genetic information foreign to S. meliloti accumulated in all identified PRSs was 6.30 Mb. However, more than 53% of this information was contained in prophages (Phs) and genomic islands (GIs) integrated into genes encoding tRNAs (tRNA genes) located on the chromosomes of the rhizobial strains studied. It was found that phiLM21-like Phs were predominantly abundant in the genomes of S. meliloti strains of distant geographical origin, whereas RR1-A- and 16-3-like Phs were much less common. In addition, GIs predominantly contained fragments of phages infecting bacteria of distant taxa, while rhizobiophage-like sequences were unique. A site-specific integration analysis revealed that not all tRNA genes in S. meliloti are integration sites, but among those in which integration occurred, there were “hot spots” of integration into which either Phs or GIs were predominantly inserted. For the first time, it is shown that at these integration “hot spots”, not only is the homology of attP and attB strictly preserved, but integrases in PRSs similar to those of phages infecting the Proteobacteria genera Azospirillum or Pseudomonas are also present. The data presented greatly expand the understanding of the fate of phage-related sequences in host bacterial genomes and also raise new questions about the role of phages in bacterial–phage coevolution. Full article
(This article belongs to the Special Issue Bacteriophage: Molecular Ecology and Pharmacology, 2nd Edition)
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