Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
7.1
4.7
Journals
Viruses
Special Issues
Biotechnological Applications of Phage and Phage-Derived Proteins 4.0
share announcement

Biotechnological Applications of Phage and Phage-Derived Proteins 4.0

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

Deadline for manuscript submissions: closed (15 April 2024) | Viewed by 6637

Special Issue Editor

Dr. Sílvio Santos

E-Mail Website
Guest Editor
Centre of Biological Engineering, University of Minho, 4710-057 Braga, Portugal
Interests: bacteriophages; genetic and protein engineering; protein functional analysis; biotechnology; pharmaceutical
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bacteriophages, the viruses of bacteria, are recognized for their potential as antimicrobial agents since their discovery, roughly a century ago, but the early inadequately controlled trials, the poor knowledge on their biology and the discovery of antibiotics has slowed phage research. In recent years, the increasing problem of multidrug-resistant bacteria has renewed and heightened interest in the use of phages as antimicrobial agents.

The recent progress in sequencing technologies, DNA manipulation and synthetic biology has equipped scientists with the necessary tools to disclose and use the powerful armamentarium of proteins that phages possess to parasite bacteria. These proteins can be used ex-phage (isolated from the phage particle) or modified/added to design phages with improved and superior characteristics and functionalities which enabled the development of new powerful applications of phages and their proteins not only in therapeutics (as new source of antimicrobials, drug delivery systems and vaccines) but also in diagnostics and materials science (for the assembly of new materials). As new phage proteins are being discovered, new valuable biotechnological applications are envisaged.

With the wide array of possibilities offered by genetic engineering and its attracting intense interest coupled with the high potential of phages, this Special Issue will focus on new biotechnological applications of phage and their derived proteins, as well on the new strategies to obtain them. Bacteriophage therapy through the use of wild type phages (without any genetic modification) is out of focus of this special issue.

Dr. Sílvio Santos
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. 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

  • bacteriophage
  • biotechnological applications
  • genetic engineering
  • antimicrobials
  • diagnostic

Published Papers (7 papers)

Download All Papers
Order results
Result details
Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:

Research

18 pages, 4295 KiB  
Article
Unraveling the Properties of Phage Display Fab Libraries and Their Use in the Selection of Gliadin-Specific Probes by Applying High-Throughput Nanopore Sequencing
by Eduardo Garcia-Calvo, Aina García-García, Santiago Rodríguez, Rosario Martín and Teresa García
Viruses 2024, 16(5), 686; https://doi.org/10.3390/v16050686 - 26 Apr 2024
Viewed by 142
Abstract
Directed evolution is a pivotal strategy for new antibody discovery, which allowed the generation of high-affinity Fabs against gliadin from two antibody libraries in our previous studies. One of the libraries was exclusively derived from celiac patients’ mRNA (immune library) while the other [...] Read more.
Directed evolution is a pivotal strategy for new antibody discovery, which allowed the generation of high-affinity Fabs against gliadin from two antibody libraries in our previous studies. One of the libraries was exclusively derived from celiac patients’ mRNA (immune library) while the other was obtained through a protein engineering approach (semi-immune library). Recent advances in high-throughput DNA sequencing techniques are revolutionizing research across genomics, epigenomics, and transcriptomics. In the present work, an Oxford Nanopore in-lab sequencing device was used to comprehensively characterize the composition of the constructed libraries, both at the beginning and throughout the phage-mediated selection processes against gliadin. A customized analysis pipeline was used to select high-quality reads, annotate chain distribution, perform sequence analysis, and conduct statistical comparisons between the different selection rounds. Some immunological attributes of the most representative phage variants after the selection process were also determined. Sequencing results revealed the successful transfer of the celiac immune response features to the immune library and the antibodies derived from it, suggesting the crucial role of these features in guiding the selection of high-affinity recombinant Fabs against gliadin. In summary, high-throughput DNA sequencing has improved our understanding of the selection processes aimed at generating molecular binders against gliadin. Full article
(This article belongs to the Special Issue Biotechnological Applications of Phage and Phage-Derived Proteins 4.0)
►▼ Show Figures

Figure 1

13 pages, 5049 KiB  
Article
Characterization of a Thermostable Endolysin of the Aeribacillus Phage AeriP45 as a Potential Staphylococcus Biofilm-Removing Agent
by Natalia N. Golosova, Yana A. Khlusevich, Vera V. Morozova, Andrey L. Matveev, Yulia N. Kozlova, Artem Y. Tikunov, Elizaveta A. Panina and Nina V. Tikunova
Viruses 2024, 16(1), 93; https://doi.org/10.3390/v16010093 - 07 Jan 2024
Viewed by 973
Abstract
Multidrug-resistant Gram-positive bacteria, including bacteria from the genus Staphylococcus, are currently a challenge for medicine. Therefore, the development of new antimicrobials is required. Promising candidates for new antistaphylococcal drugs are phage endolysins, including endolysins from thermophilic phages against other Gram-positive bacteria. In [...] Read more.
Multidrug-resistant Gram-positive bacteria, including bacteria from the genus Staphylococcus, are currently a challenge for medicine. Therefore, the development of new antimicrobials is required. Promising candidates for new antistaphylococcal drugs are phage endolysins, including endolysins from thermophilic phages against other Gram-positive bacteria. In this study, the recombinant endolysin LysAP45 from the thermophilic Aeribacillus phage AP45 was obtained and characterized. The recombinant endolysin LysAP45 was produced in Escherichia coli M15 cells. It was shown that LysAP45 is able to hydrolyze staphylococcal peptidoglycans from five species and eleven strains. Thermostability tests showed that LysAP45 retained its hydrolytic activity after incubation at 80 °C for at least 30 min. The enzymatically active domain of the recombinant endolysin LysAP45 completely disrupted biofilms formed by multidrug-resistant S. aureus, S. haemolyticus, and S. epidermidis. The results suggested that LysAP45 is a novel thermostable antimicrobial agent capable of destroying biofilms formed by various species of multidrug-resistant Staphylococcus. An unusual putative cell-binding domain was found at the C-terminus of LysAP45. No domains with similar sequences were found among the described endolysins. Full article
(This article belongs to the Special Issue Biotechnological Applications of Phage and Phage-Derived Proteins 4.0)
►▼ Show Figures

Figure 1

12 pages, 2241 KiB  
Article
Experimental Identification of Cross-Reacting IgG Hotspots to Predict Existing Immunity Evasion of SARS-CoV-2 Variants by a New Biotechnological Application of Phage Display
by Marek Adam Harhala, Katarzyna Gembara, Krzysztof Baniecki, Aleksandra Pikies, Artur Nahorecki, Natalia Jędruchniewicz, Zuzanna Kaźmierczak, Izabela Rybicka, Tomasz Klimek, Wojciech Witkiewicz, Kamil Barczyk, Marlena Kłak and Krystyna Dąbrowska
Viruses 2024, 16(1), 58; https://doi.org/10.3390/v16010058 - 29 Dec 2023
Viewed by 860
Abstract
Multiple pathogens are competing against the human immune response, leading to outbreaks that are increasingly difficult to control. For example, the SARS-CoV-2 virus continually evolves, giving rise to new variants. The ability to evade the immune system is a crucial factor contributing to [...] Read more.
Multiple pathogens are competing against the human immune response, leading to outbreaks that are increasingly difficult to control. For example, the SARS-CoV-2 virus continually evolves, giving rise to new variants. The ability to evade the immune system is a crucial factor contributing to the spread of these variants within the human population. With the continuous emergence of new variants, it is challenging to comprehend all the possible combinations of previous infections, various vaccination types, and potential exposure to new variants in an individual patient. Rather than conducting variant-to-variant comparisons, an efficient approach could involve identifying key protein regions associated with the immune evasion of existing immunity against the virus. In this study, we propose a new biotechnological application of bacteriophages, the phage display platform for experimental identification of regions (linear epitopes) that may function as cross-reacting IgG hotspots in SARS-CoV-2 structural proteins. A total of 34,949 epitopes derived from genomes of all SARS-CoV-2 variants deposited prior to our library design were tested in a single assay. Cross-reacting IgG hotspots are protein regions frequently recognized by cross-reacting antibodies in many variants. The assay facilitated the one-step identification of immunogenic regions of proteins that effectively induced specific IgG in SARS-CoV-2-infected patients. We identified four regions demonstrating both significant immunogenicity and the activity of a cross-reacting IgG hotspot in protein S (located at NTD, RBD, HR1, and HR2/TM domains) and two such regions in protein N (at 197–280 and 358–419 aa positions). This novel method for identifying cross-reacting IgG hotspots holds promise for informing vaccine design and serological diagnostics for COVID-19 and other infectious diseases. Full article
(This article belongs to the Special Issue Biotechnological Applications of Phage and Phage-Derived Proteins 4.0)
►▼ Show Figures

Figure 1

15 pages, 2616 KiB  
Article
Development of a Replication-Deficient Bacteriophage Reporter Lacking an Essential Baseplate Wedge Subunit
by Jose Gil, John Paulson, Henriett Zahn, Matthew Brown, Minh M. Nguyen and Stephen Erickson
Viruses 2024, 16(1), 8; https://doi.org/10.3390/v16010008 - 20 Dec 2023
Viewed by 930
Abstract
Engineered bacteriophages (phages) can be effective diagnostic reporters for detecting a variety of bacterial pathogens. Although a promising biotechnology, the large-scale use of these reporters may result in the unintentional release of genetically modified viruses. In order to limit the potential environmental impact, [...] Read more.
Engineered bacteriophages (phages) can be effective diagnostic reporters for detecting a variety of bacterial pathogens. Although a promising biotechnology, the large-scale use of these reporters may result in the unintentional release of genetically modified viruses. In order to limit the potential environmental impact, the ability of these phages to propagate outside the laboratory was targeted. The phage SEA1 has been previously engineered to facilitate food safety as an accurate and sensitive reporter for Salmonella contamination. In this study, homologous recombination was used to replace the expression of an essential baseplate wedge subunit (gp141) in SEA1 with a luciferase, NanoLuc®. This reporter, referred to as SEA1Δgp141.NL, demonstrated a loss of plaque formation and a failure to increase in titer following infection of Salmonella. SEA1Δgp141.NL was thus incapable of producing infectious progeny in the absence of gp141. In contrast, production of high titer stocks was possible when gp141 was artificially supplied in trans during infection. As a reporter, SEA1Δgp141.NL facilitated rapid, sensitive, and robust detection of Salmonella despite an inability to replicate. These results suggest that replication-deficient reporter phages are an effective method to obtain improved containment without sacrificing significant performance or the ease of production associated with many phage-based diagnostic methods. Full article
(This article belongs to the Special Issue Biotechnological Applications of Phage and Phage-Derived Proteins 4.0)
►▼ Show Figures

Figure 1

15 pages, 1698 KiB  
Article
Alginate-Encapsulated Mycobacteriophage: A Potential Approach for the Management of Intestinal Mycobacterial Disease
by Laura Michelle O’Connell, Aidan Coffey and Jim O’Mahony
Viruses 2023, 15(12), 2290; https://doi.org/10.3390/v15122290 - 22 Nov 2023
Viewed by 763
Abstract
Encapsulated medication is a common method of administering therapeutic treatments. As researchers explore alternative therapies, it is likely that encapsulation will remain a feature of these novel treatments, particularly when routes of delivery are considered. For instance, alginate-encapsulation is often favoured where gastric [...] Read more.
Encapsulated medication is a common method of administering therapeutic treatments. As researchers explore alternative therapies, it is likely that encapsulation will remain a feature of these novel treatments, particularly when routes of delivery are considered. For instance, alginate-encapsulation is often favoured where gastric digestion poses an obstacle. When exposed to cations (namely Ca2+), alginate readily forms gels that are resilient to acidic conditions and readily dissociate in response to mid-range pH. This action can be extremely valuable for the encapsulation of phages. The efficient delivery of phages to the intestine is important when considering mycobacteriophage (MP) therapy (or MP prophylaxis) for disseminated mycobacterial infections and chronic gastroenteritis conditions. This study presents the design and in vitro validation of an alginate-encapsulated MP capable of releasing phages in a pH-dependent manner. Ultimately, it is shown that encapsulated phages pretreated with simulated gastric fluid (SGF) are capable of releasing viable phages into simulated intestinal fluid (SIF) and thereby reducing the mycobacterial numbers in spiked SIF by 90%. These findings suggest that alginate encapsulation may be a viable option for therapeutic and prophylactic approaches to the management of intestinal mycobacterial disease, such as Johne’s disease. Full article
(This article belongs to the Special Issue Biotechnological Applications of Phage and Phage-Derived Proteins 4.0)
►▼ Show Figures

Figure 1

20 pages, 4836 KiB  
Article
Characterization of Lactobacilli Phage Endolysins and Their Functional Domains–Potential Live Biotherapeutic Testing Reagents
by Robert J. Dorosky, Stephanie L. Lola, Haleigh A. Brown, Jeremy E. Schreier, Sheila M. Dreher-Lesnick and Scott Stibitz
Viruses 2023, 15(10), 1986; https://doi.org/10.3390/v15101986 - 23 Sep 2023
Viewed by 1224
Abstract
Phage endolysin-specific binding characteristics and killing activity support their potential use in biotechnological applications, including potency and purity testing of live biotherapeutic products (LBPs). LBPs contain live organisms, such as lactic acid bacteria (LAB), and are intended for use as drugs. Our approach [...] Read more.
Phage endolysin-specific binding characteristics and killing activity support their potential use in biotechnological applications, including potency and purity testing of live biotherapeutic products (LBPs). LBPs contain live organisms, such as lactic acid bacteria (LAB), and are intended for use as drugs. Our approach uses the endolysin cell wall binding domains (CBD) for LBP potency assays and the endolysin killing activity for purity assays. CBDs of the following five lactobacilli phage lysins were characterized: CL1, Jlb1, Lj965, LL-H, and ΦJB. They exhibited different bindings to 27 LAB strains and were found to bind peptidoglycan or surface polymers. Flow cytometry based on CBD binding was used to enumerate viable counts of two strains in the mixture. CL1-lys, jlb1-lys, and ΦJB-lys and their enzymatic domains (EADs) exhibited cell wall digestive activity and lytic activity against LAB. Jlb1-EAD and ΦJB-EAD were more sensitive than their respective hololysins to buffer pH and NaCl changes. The ΦJB-EAD exhibited stronger lytic activity than ΦJB-lys, possibly due to ΦJB-CBD-mediated sequestration of ΦJB-lys by cell debris. CBD multiplex assays indicate that these proteins may be useful LBP potency reagents, and the lytic activity suggests that CL1-lys, jlb1-lys, and ΦJB-lys and their EADs are good candidates for LBP purity reagent development. Full article
(This article belongs to the Special Issue Biotechnological Applications of Phage and Phage-Derived Proteins 4.0)
►▼ Show Figures

Figure 1

19 pages, 3444 KiB  
Article
Evolutionary Qβ Phage Displayed Nanotag Library and Peptides for Biosensing
by Augustin Ntemafack, Aristide Dzelamonyuy, Godwin Nchinda and Alain Bopda Waffo
Viruses 2023, 15(7), 1414; https://doi.org/10.3390/v15071414 - 22 Jun 2023
Cited by 1 | Viewed by 1171
Abstract
We selected a novel biotin-binding peptide for sensing biotin, biotinylated proteins, and nucleotides. From a 15-mer library displayed on the RNA coliphage Qβ, a 15-amino acid long peptide (HGHGWQIPVWPWGQG) hereby referred to as a nanotag was identified to selectively bind biotin. The target [...] Read more.
We selected a novel biotin-binding peptide for sensing biotin, biotinylated proteins, and nucleotides. From a 15-mer library displayed on the RNA coliphage Qβ, a 15-amino acid long peptide (HGHGWQIPVWPWGQG) hereby referred to as a nanotag was identified to selectively bind biotin. The target selection was achieved through panning with elution by infection. The selected peptide was tested as a transducer for an immunogenic epitope of the foot-and-mouth disease virus (FMDV) on Qβ phage platform separated by a linker. The biotin-tag showed no significant influence on the affinity of the epitope to its cognate antibody (SD6). The nanotag-bound biotin selectively fused either to the C- or N-terminus of the epitope. The epitope would not bind or recognize SD6 while positioned at the N-terminus of the nanotag. Additionally, the biotin competed linearly with the SD6 antibody in a competitive ELISA. Competition assays using the selected recombinant phage itself as a probe or transducer enable the operationalization of this technology as a biosensor toolkit to sense and quantify SD6 analyte. Herein, the published Strep II nanotag (DVEWLDERVPLVET) was used as a control and has similar functionalities to our proposed novel biotin-tag thereby providing a new platform for developing devices for diagnostic purposes. Full article
(This article belongs to the Special Issue Biotechnological Applications of Phage and Phage-Derived Proteins 4.0)
►▼ Show Figures

Figure 1

Show export options expand_more Show export options expand_less
Select all
Export citation of selected articles as:
 
Displaying articles 1-7
Back to TopTop