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Bacteriophage—Molecular Studies 2.0

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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 December 2020) | Viewed by 38710

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Dr. Alicja Wegrzyn

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Institute of Biochemistry and Biophysics of the Polish Academy of Sciences, Gdansk, Poland
Interests: biology of bacteriophages; biodiversity of bacteriophages; regulation of bacteriophage development; regulation of phage gene expression; control of phage DNA replication; phage therapy; phages bearing genes of toxins; bacteriophage genomics
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Dear Colleagues,

Bacteriophages, the viruses infecting bacterial cells, were first described 100 years ago, in 1915, by Frederick Twort. The scientist who introduced the name “bacteriophage” was Felix d’Herelle, who investigated these viruses for many years, leading to new fields of research, including bacteriophage therapy. In the following years, bacteriophages became important model organisms in molecular biology and genetics. Many basic discoveries were made during studies of these viruses, with spectacular results, such as demonstrating that DNA is a genetic material, that viruses can encode enzymes, that gene expression proceeds through mRNA molecules, that the genetic code is based on nucleotide triplets, that gene expression can be regulated by transcription antitermination, that specific genes encode heat shock proteins, and that specific mechanisms regulate DNA replication initiation based on the formation and rearrangement of protein–DNA complexes. The regulatory processes occurring in bacteriophage-infected cells have been considered paradigms of the control of developmental pathways. On the other hand, the history of research on bacteriophages also passed through dark times when, at the end of 20^th century, there was the collective impression that we knew almost everything there was to know about these simple viruses, and that it was time to investigate more complex organisms instead. Nevertheless, subsequent discoveries have indicated that such an assumption was unequivocally false, and studies on the molecular biology and biotechnology of bacteriophages have once again become extensive. Interest in these viruses has increased dramatically, and it appears that we are far from understanding the biology of the vast majority of bacteriophages.

This Special Issue of International Journal of Molecular Sciences is devoted to publishing papers on studies of bacteriophages at the molecular level. Papers on phage biodiversity, regulation of processes occurring during phage development, and the practical use of bacteriophages—including biotechnology and phage therapy—are welcome, providing the studies deal with the molecular level and utilize molecular biology methods. I am hopeful of building a great collection of articles devoted to recent discoveries in the field of bacteriophage molecular biology. Therefore, I invite you to submit manuscripts to this Special Issue as an excellent forum to share your discoveries in this fascinating research field.

Dr. Alicja Wegrzyn
Guest Editor

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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.

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Keywords

bacteriophage biodiversity
regulation of bacteriophage development
molecular processes in bacteriophages
bacteriophage-based biotechnology
phage therapy

Related Special Issues

Bacteriophage—Molecular Studies 4.0 in International Journal of Molecular Sciences (12 articles)
Bacteriophage—Molecular Studies 5.0 in International Journal of Molecular Sciences (12 articles)
Bacteriophage—Molecular Studies 6.0 in International Journal of Molecular Sciences

Published Papers (10 papers)

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Research

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24 pages, 3561 KiB

Open AccessArticle

Extraordinary Multi-Organismal Interactions Involving Bacteriophages, Bacteria, Fungi, and Rotifers: Quadruple Microbial Trophic Network in Water Droplets

by Katarzyna Turnau, Edyta Fiałkowska, Rafał Ważny, Piotr Rozpądek, Grzegorz Tylko, Sylwia Bloch, Bożena Nejman-Faleńczyk, Michał Grabski, Alicja Węgrzyn and Grzegorz Węgrzyn

Int. J. Mol. Sci. 2021, 22(4), 2178; https://doi.org/10.3390/ijms22042178 - 22 Feb 2021

Cited by 8 | Viewed by 4636

Abstract

Our observations of predatory fungi trapping rotifers in activated sludge and laboratory culture allowed us to discover a complicated trophic network that includes predatory fungi armed with bacteria and bacteriophages and the rotifers they prey on. Such a network seems to be common in various habitats, although it remains mostly unknown due to its microscopic size. In this study, we isolated and identified fungi and bacteria from activated sludge. We also noticed abundant, virus-like particles in the environment. The fungus developed absorptive hyphae within the prey. The bacteria showed the ability to enter and exit from the hyphae (e.g., from the traps into the caught prey). Our observations indicate that the bacteria and the fungus share nutrients obtained from the rotifer. To narrow the range of bacterial strains isolated from the mycelium, the effects of bacteria supernatants and lysed bacteria were studied. Bacteria isolated from the fungus were capable of immobilizing the rotifer. The strongest negative effect on rotifer mobility was shown by a mixture of Bacillus sp. and Stenotrophomonas maltophilia. The involvement of bacteriophages in rotifer hunting was demonstrated based on molecular analyses and was discussed. The described case seems to be an extraordinary quadruple microbiological puzzle that has not been described and is still far from being understood. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 2.0)

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10 pages, 1434 KiB

Open AccessArticle

Tumor-Targeting Peptides Search Strategy for the Delivery of Therapeutic and Diagnostic Molecules to Tumor Cells

by Maria D. Dmitrieva, Anna A. Voitova, Maya A. Dymova, Vladimir A. Richter and Elena V. Kuligina

Int. J. Mol. Sci. 2021, 22(1), 314; https://doi.org/10.3390/ijms22010314 - 30 Dec 2020

Cited by 9 | Viewed by 2435

Abstract

Background: The combination of the unique properties of cancer cells makes it possible to find specific ligands that interact directly with the tumor, and to conduct targeted tumor therapy. Phage display is one of the most common methods for searching for specific ligands. Bacteriophages display peptides, and the peptides themselves can be used as targeting molecules for the delivery of diagnostic and therapeutic agents. Phage display can be performed both in vitro and in vivo. Moreover, it is possible to carry out the phage display on cells pre-enriched for a certain tumor marker, for example, CD44 and CD133. Methods: For this work we used several methods, such as phage display, sequencing, cell sorting, immunocytochemistry, phage titration. Results: We performed phage display using different screening systems (in vitro and in vivo), different phage libraries (Ph.D-7, Ph.D-12, Ph.D-C7C) on CD44+/CD133+ and without enrichment U-87 MG cells. The binding efficiency of bacteriophages displayed tumor-targeting peptides on U-87 MG cells was compared in vitro. We also conducted a comparative analysis in vivo of the specificity of the accumulation of selected bacteriophages in the tumor and in the control organs (liver, brain, kidney and lungs). Conclusions: The screening in vivo of linear phage peptide libraries for glioblastoma was the most effective strategy for obtaining tumor-targeting peptides providing targeted delivery of diagnostic and therapeutic agents to glioblastoma. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 2.0)

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21 pages, 6571 KiB

Open AccessArticle

Bacteriophages vB_Sen-TO17 and vB_Sen-E22, Newly Isolated Viruses from Chicken Feces, Specific for Several Salmonella enterica Strains

by Katarzyna Kosznik-Kwaśnicka, Łukasz Grabowski, Michał Grabski, Mateusz Kaszubski, Marcin Górniak, Agata Jurczak-Kurek, Grzegorz Węgrzyn and Alicja Węgrzyn

Int. J. Mol. Sci. 2020, 21(22), 8821; https://doi.org/10.3390/ijms21228821 - 21 Nov 2020

Cited by 14 | Viewed by 2547

Abstract

Two newly discovered bacteriophages, isolated from chicken feces and infecting Salmonella enterica strains, are described in this report. These phages have been named vB_Sen-TO17 and vB_Sen-E22, and we present their molecular and functional characterization. Both studied viruses are able to infect several S. enterica strains and develop lytically, but their specific host ranges differ significantly. Electron microscopic analyses of virions have been performed, and full genome sequences were determined and characterized, along with molecular phylogenetic studies. Genomes of vB_Sen-TO17 (ds DNA of 41,658 bp) and vB_Sen-E22 (dsDNA of 108,987 bp) are devoid of homologs of any known or putative gene coding for toxins or any other proteins potentially deleterious for eukaryotic cells. Both phages adsorbed efficiently (>95% adsorbed virions) within 10 min at 42 °C (resembling chicken body temperature) on cells of most tested host strains. Kinetics of lytic development of vB_Sen-TO17 and vB_Sen-E22, determined in one-step growth experiments, indicated that development is complete within 30–40 min at 42 °C, whereas burst sizes vary from 9 to 79 progeny phages per cell for vB_Sen-TO17 and from 18 to 64 for vB_Sen-E22, depending on the host strain. Virions of both phages were relatively stable (from several percent to almost 100% survivability) under various conditions, including acidic and alkaline pH values (from 3 to 12), temperatures from −80 °C to 60 °C, 70% ethanol, chloroform, and 10% DMSO. These characteristics of vB_Sen-TO17 and vB_Sen-E22 indicate that these phages might be considered in further studies on phage therapy, particularly in attempts to eliminate S. enterica from chicken intestine. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 2.0)

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28 pages, 4074 KiB

Open AccessArticle

Identification, Characterization, and Genomic Analysis of Novel Serratia Temperate Phages from a Gold Mine

by Katarzyna Bujak, Przemyslaw Decewicz, Jerzy Kaminski and Monika Radlinska

Int. J. Mol. Sci. 2020, 21(18), 6709; https://doi.org/10.3390/ijms21186709 - 13 Sep 2020

Cited by 11 | Viewed by 4490

Abstract

Bacteria of the genus Serratia inhabit a variety of ecological niches like water, soil, and the bodies of animals, and have a wide range of lifestyles. Currently, the complete genome sequences of 25 Serratia phages are available in the NCBI database. All of them were isolated from nutrient-rich environments like sewage, with the use of clinical Serratia strains as hosts. In this study, we identified a novel Serratia myovirus named vB_SspM_BZS1. Both the phage and its host Serratia sp. OS31 were isolated from the same oligotrophic environment, namely, an abandoned gold mine (Zloty Stok, Poland). The BZS1 phage was thoroughly characterized here in terms of its genomics, morphology, and infection kinetics. We also demonstrated that Serratia sp. OS31 was lysogenized by mitomycin-inducible siphovirus vB_SspS_OS31. Comparative analyses revealed that vB_SspM_BZS1 and vB_SspS_OS31 were remote from the known Serratia phages. Moreover, vB_SspM_BZS1 was only distantly related to other viruses. However, we discovered similar prophage sequences in genomes of various bacteria here. Additionally, a protein-based similarity network showed a high diversity of Serratia phages in general, as they were scattered across nineteen different clusters. In summary, this work broadened our knowledge on the diverse relationships of Serratia phages. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 2.0)

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27 pages, 4135 KiB

Open AccessArticle

Characterization of the Bacteriophage vB_EfaS-271 Infecting Enterococcus faecalis

by Gracja Topka-Bielecka, Sylwia Bloch, Bożena Nejman-Faleńczyk, Michał Grabski, Agata Jurczak-Kurek, Marcin Górniak, Aleksandra Dydecka, Agnieszka Necel, Grzegorz Węgrzyn and Alicja Węgrzyn

Int. J. Mol. Sci. 2020, 21(17), 6345; https://doi.org/10.3390/ijms21176345 - 1 Sep 2020

Cited by 12 | Viewed by 3663

Abstract

A newly isolated bacteriophage infecting Enterococcus faecalis strains has been characterized, including determination of its molecular features. This phage, named vB_EfaS-271, has been classified as a Siphoviridae member, according to electron microscopy characterization of the virions, composed of a 50 nm-diameter head and a long, flexible, noncontractable tail (219 × 12.5 nm). Analysis of the whole dsDNA genome of this phage showed that it consists of 40,197 bp and functional modules containing genes coding for proteins that are involved in DNA replication (including DNA polymerase/primase), morphogenesis, packaging and cell lysis. Mass spectrometry analysis allowed us to identify several phage-encoded proteins. vB_EfaS-271 reveals a relatively narrow host range, as it is able to infect only a few E. faecalis strains. On the other hand, it is a virulent phage (unable to lysogenize host cells), effectively and quickly destroying cultures of sensitive host bacteria, with a latent period as short as 8 min and burst size of approximately 70 phages per cell at 37 °C. This phage was also able to destroy biofilms formed by E. faecalis. These results contribute to our understanding of the biodiversity of bacteriophages, confirming the high variability among these viruses and indicating specific genetic and functional features of vB_EfaS-271. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 2.0)

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20 pages, 1299 KiB

Open AccessArticle

Isolation and Characterization of the Novel Bacteriophage AXL3 against Stenotrophomonas maltophilia

by Jaclyn G. McCutcheon, Andrea Lin and Jonathan J. Dennis

Int. J. Mol. Sci. 2020, 21(17), 6338; https://doi.org/10.3390/ijms21176338 - 1 Sep 2020

Cited by 25 | Viewed by 5229

Abstract

The rapid increase in the number of worldwide human infections caused by the extremely antibiotic resistant bacterial pathogen Stenotrophomonas maltophilia is cause for concern. An alternative treatment solution in the post-antibiotic era is phage therapy, the use of bacteriophages to selectively kill bacterial pathogens. In this study, the novel bacteriophage AXL3 (vB_SmaS-AXL_3) was isolated from soil and characterized. Host range analysis using a panel of 29 clinical S. maltophilia isolates shows successful infection of five isolates and electron microscopy indicates that AXL3 is a member of the Siphoviridae family. Complete genome sequencing and analysis reveals a 47.5 kb genome predicted to encode 65 proteins. Functionality testing suggests AXL3 is a virulent phage and results show that AXL3 uses the type IV pilus, a virulence factor on the cell surface, as its receptor across its host range. This research identifies a novel virulent phage and characterization suggests that AXL3 is a promising phage therapy candidate, with future research examining modification through genetic engineering to broaden its host range. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 2.0)

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14 pages, 5253 KiB

Open AccessArticle

Exhaustive Search of the Receptor Ligands by the CyCLOPS (Cytometry Cell-Labeling Operable Phage Screening) Technique

by Irina A. Ishina, Ioanna N. Filimonova, Maria Y. Zakharova, Leyla A. Ovchinnikova, Azad E. Mamedov, Yakov A. Lomakin and Alexey A. Belogurov, Jr.

Int. J. Mol. Sci. 2020, 21(17), 6258; https://doi.org/10.3390/ijms21176258 - 29 Aug 2020

Cited by 5 | Viewed by 2840

Abstract

Effective and versatile screening of the peptide ligands capable of selectively binding to diverse receptors is in high demand for the state-of-the-art technologies in life sciences, including probing of specificity of the cell surface receptors and drug development. Complex microenvironment and structure of the surface receptors significantly reduce the possibility to determine their specificity, especially when in vitro conditions are utilized. Previously, we designed a publicly available platform for the ultra-high-throughput screening (uHTS) of the specificity of surface-exposed receptors of the living eukaryotic cells, which was done by consolidating the phage display and flow cytometry techniques. Here, we significantly improved this methodology and designed the fADL-1e-based phage vectors that do not require a helper hyperphage for the virion assembly. The enhanced screening procedure was tested on soluble human leukocyte antigen (HLA) class II molecules and transgenic antigen-specific B cells that express recombinant lymphoid B-cell receptor (BCR). Our data suggest that the improved vector system may be successfully used for the comprehensive search of the receptor ligands in either cell-based or surface-immobilized assays. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 2.0)

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26 pages, 6811 KiB

Open AccessArticle

Characteristics of a Series of Three Bacteriophages Infecting Salmonella enterica Strains

by Katarzyna Kosznik-Kwaśnicka, Karolina Ciemińska, Michał Grabski, Łukasz Grabowski, Marcin Górniak, Agata Jurczak-Kurek, Grzegorz Węgrzyn and Alicja Węgrzyn

Int. J. Mol. Sci. 2020, 21(17), 6152; https://doi.org/10.3390/ijms21176152 - 26 Aug 2020

Cited by 20 | Viewed by 3121

Abstract

Molecular and functional characterization of a series of three bacteriophages, vB_SenM-1, vB_SenM-2, and vB_SenS-3, infecting various Salmonella enterica serovars and strains is presented. All these phages were able to develop lytically while not forming prophages. Moreover, they were able to survive at pH 3. The phages revealed different host ranges within serovars and strains of S. enterica, different adsorption rates on host cells, and different lytic growth kinetics at various temperatures (in the range of 25 to 42 °C). They efficiently reduced the number of cells in the bacterial biofilm and decreased the biofilm mass. Whole genome sequences of these phages have been determined and analyzed, including their phylogenetic relationships. In conclusion, we have demonstrated detailed characterization of a series of three bacteriophages, vB_SenM-1, vB_SenM-2, and vB_SenS-3, which reveal favorable features in light of their potential use in phage therapy of humans and animals, as well as for food protection purposes. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 2.0)

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42 pages, 17357 KiB

Open AccessArticle

Phage S144, a New Polyvalent Phage Infecting Salmonella spp. and Cronobacter sakazakii

by Michela Gambino, Anders Nørgaard Sørensen, Stephen Ahern, Georgios Smyrlis, Yilmaz Emre Gencay, Hanne Hendrix, Horst Neve, Jean-Paul Noben, Rob Lavigne and Lone Brøndsted

Int. J. Mol. Sci. 2020, 21(15), 5196; https://doi.org/10.3390/ijms21155196 - 22 Jul 2020

Cited by 21 | Viewed by 5026

Abstract

Phages are generally considered species- or even strain-specific, yet polyvalent phages are able to infect bacteria from different genera. Here, we characterize the novel polyvalent phage S144, a member of the Loughboroughvirus genus. By screening 211 Enterobacteriaceae strains, we found that phage S144 forms plaques on specific serovars of Salmonella enterica subsp. enterica and on Cronobacter sakazakii. Analysis of phage resistant mutants suggests that the O-antigen of lipopolysaccharide is the phage receptor in both bacterial genera. The S144 genome consists of 53,628 bp and encodes 80 open reading frames (ORFs), but no tRNA genes. In total, 32 ORFs coding for structural proteins were confirmed by ESI-MS/MS analysis, whereas 45 gene products were functionally annotated within DNA metabolism, packaging, nucleotide biosynthesis and phage morphogenesis. Transmission electron microscopy showed that phage S144 is a myovirus, with a prolate head and short tail fibers. The putative S144 tail fiber structure is, overall, similar to the tail fiber of phage Mu and the C-terminus shows amino acid similarity to tail fibers of otherwise unrelated phages infecting Cronobacter. Since all phages in the Loughboroughvirus genus encode tail fibers similar to S144, we suggest that phages in this genus infect Cronobacter sakazakii and are polyvalent. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 2.0)

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Review

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17 pages, 2266 KiB

Open AccessReview

Phage Display to Augment Biomaterial Function

by Thomas A. Davidson, Samantha J. McGoldrick and David H. Kohn

Int. J. Mol. Sci. 2020, 21(17), 5994; https://doi.org/10.3390/ijms21175994 - 20 Aug 2020

Cited by 12 | Viewed by 3740

Abstract

Biomaterial design relies on controlling interactions between materials and their biological environments to modulate the functions of proteins, cells, and tissues. Phage display is a powerful tool that can be used to discover peptide sequences with high affinity for a desired target. When incorporated into biomaterial design, peptides identified via phage display can functionalize material surfaces to control the interaction between a biomaterial and its local microenvironment. A targeting peptide has high specificity for a given target, allowing for homing a specific protein, cell, tissue, or other material to a biomaterial. A functional peptide has an affinity for a given protein, cell, or tissue, but also modulates its target’s activity upon binding. Biomaterials can be further enhanced using a combination of targeting and/or functional peptides to create dual-functional peptides for bridging two targets or modulating the behavior of a specific protein or cell. This review will examine current and future applications of phage display for the augmentation of biomaterials. Full article

(This article belongs to the Special Issue Bacteriophage—Molecular Studies 2.0)

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