Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
5.5
4.8
Journals
Antibiotics
Special Issues
Development of Bacteriophage Derived Lysins and Depolymerases for Therapeutic Purposes...
share announcement

Development of Bacteriophage Derived Lysins and Depolymerases for Therapeutic Purposes in Combating Bacterial Pathogens

A special issue of Antibiotics (ISSN 2079-6382). This special issue belongs to the section "Bacteriophages".

Deadline for manuscript submissions: closed (1 October 2021) | Viewed by 23064

Special Issue Editor

Dr. Hugo Oliveira

E-Mail Website
Guest Editor
Centre of Biological Engineering, University of Minho, Braga, Portugal
Interests: bacteriophages; phage-dervied proteins; bacterial infections; genomics; proteomics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Bacterial infections have been increasing over the years, being considered as a huge health problem worldwide. This is particularly due to the increase in the resistance to antibiotics, which lead to less effective treatments. Consequently, new strategies are needed to control multi-drug resistant bacteria.

Bacteriophage-derived proteins can be seen as an appealing alternative treatment. Bacteriophages are viruses that encode several specialized proteins that break down several host carbohydrate barriers, allowing them to enter, replicate and lyse their bacterial hosts. First, polysaccharide depolymerases degrade capsules, lipopolysaccharides or exopolysaccharides, allowing phages to reach the inner cell layers. Second, virion-associated lysins come into play by locally degrading the peptidoglycan, enabling phages to inject their DNA inside the cell and replicate. Finally, endolysins are produced at the end of the phage lytic cycle to quickly degrade the peptidoglycan, causing the cells to burst and the progeny to be subsequently released.

This Special Issue seeks manuscript submissions that further our understanding of how these enzymes could be used to target different bacterial polysaccharides (capsules, lipopolysaccharides, exopolysaccharides and peptidoglycan), to control bacterial pathogens in food, veterinary and human medicine.

Dr. Hugo Oliveira
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. Antibiotics 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 2900 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

  • Bacteriophages
  • Virion-assiociated lysins
  • Polysaccharide depolymerases
  • Endolysins
  • Bacterial infections

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

20 pages, 5511 KiB  
Article
The Specific Capsule Depolymerase of Phage PMK34 Sensitizes Acinetobacter baumannii to Serum Killing
by Karim Abdelkader, Diana Gutiérrez, Agnieszka Latka, Dimitri Boeckaerts, Zuzanna Drulis-Kawa, Bjorn Criel, Hans Gerstmans, Amal Safaan, Ahmed S. Khairalla, Yasser Gaber, Tarek Dishisha and Yves Briers
Antibiotics 2022, 11(5), 677; https://doi.org/10.3390/antibiotics11050677 - 17 May 2022
Cited by 8 | Viewed by 2916
Abstract
The rising antimicrobial resistance is particularly alarming for Acinetobacter baumannii, calling for the discovery and evaluation of alternatives to treat A. baumannii infections. Some bacteriophages produce a structural protein that depolymerizes capsular exopolysaccharide. Such purified depolymerases are considered as novel antivirulence compounds. [...] Read more.
The rising antimicrobial resistance is particularly alarming for Acinetobacter baumannii, calling for the discovery and evaluation of alternatives to treat A. baumannii infections. Some bacteriophages produce a structural protein that depolymerizes capsular exopolysaccharide. Such purified depolymerases are considered as novel antivirulence compounds. We identified and characterized a depolymerase (DpoMK34) from Acinetobacter phage vB_AbaP_PMK34 active against the clinical isolate A. baumannii MK34. In silico analysis reveals a modular protein displaying a conserved N-terminal domain for anchoring to the phage tail, and variable central and C-terminal domains for enzymatic activity and specificity. AlphaFold-Multimer predicts a trimeric protein adopting an elongated structure due to a long α-helix, an enzymatic β-helix domain and a hypervariable 4 amino acid hotspot in the most ultimate loop of the C-terminal domain. In contrast to the tail fiber of phage T3, this hypervariable hotspot appears unrelated with the primary receptor. The functional characterization of DpoMK34 revealed a mesophilic enzyme active up to 50 °C across a wide pH range (4 to 11) and specific for the capsule of A. baumannii MK34. Enzymatic degradation of the A. baumannii MK34 capsule causes a significant drop in phage adsorption from 95% to 9% after 5 min. Although lacking intrinsic antibacterial activity, DpoMK34 renders A. baumannii MK34 fully susceptible to serum killing in a serum concentration dependent manner. Unlike phage PMK34, DpoMK34 does not easily select for resistant mutants either against PMK34 or itself. In sum, DpoMK34 is a potential antivirulence compound that can be included in a depolymerase cocktail to control difficult to treat A. baumannii infections. Full article
(This article belongs to the Special Issue Development of Bacteriophage Derived Lysins and Depolymerases for Therapeutic Purposes in Combating Bacterial Pathogens)
►▼ Show Figures

Graphical abstract

12 pages, 1781 KiB  
Article
Unpuzzling Friunavirus-Host Interactions One Piece at a Time: Phage Recognizes Acinetobacter pittii via a New K38 Capsule Depolymerase
by Rita Domingues, Ana Barbosa, Sílvio B. Santos, Diana Priscila Pires, Jonathan Save, Grégory Resch, Joana Azeredo and Hugo Oliveira
Antibiotics 2021, 10(11), 1304; https://doi.org/10.3390/antibiotics10111304 - 26 Oct 2021
Cited by 3 | Viewed by 2205
Abstract
Acinetobacter pittii is a species that belong to the Acinetobacter calcoaceticus-baumannii complex, increasingly recognized as major nosocomial bacterial pathogens, often associated with multiple drug-resistances. The capsule surrounding the bacteria represents a main virulence factor, helping cells avoid phage predation and host immunity. Accordingly, [...] Read more.
Acinetobacter pittii is a species that belong to the Acinetobacter calcoaceticus-baumannii complex, increasingly recognized as major nosocomial bacterial pathogens, often associated with multiple drug-resistances. The capsule surrounding the bacteria represents a main virulence factor, helping cells avoid phage predation and host immunity. Accordingly, a better understanding of the phage infection mechanisms is required to efficiently develop phage therapy against Acinetobacter of different capsular types. Here, we report the isolation of the novel A. pittii-infecting Fri1-like phage vB_Api_3043-K38 (3043-K38) of the Podoviridae morphotype, from sewage samples. Its 41,580 bp linear double-stranded DNA genome harbours 53 open reading frames and 302 bp of terminal repeats. We show that all studied Acinetobacter Fri1-like viruses have highly similar genomes, which differentiate only at the genes coding for tailspike, likely to adapt to different host receptors. The isolated phage 3043-K38 specifically recognizes an untapped Acinetobacter K38 capsule type via a novel tailspike with K38 depolymerase activity. The recombinant K38 depolymerase region of the tailspike (center-end region) forms a thermostable trimer, and quickly degrades capsules. When the K38 depolymerase is applied to the cells, it makes them resistant to phage predation. Interestingly, while K38 depolymerase treatments do not synergize with antibiotics, it makes bacterial cells highly susceptible to the host serum complement. In summary, we characterized a novel phage-encoded K38 depolymerase, which not only advances our understanding of phage-host interactions, but could also be further explored as a new antibacterial agent against drug-resistant Acinetobacter. Full article
(This article belongs to the Special Issue Development of Bacteriophage Derived Lysins and Depolymerases for Therapeutic Purposes in Combating Bacterial Pathogens)
►▼ Show Figures

Figure 1

14 pages, 2144 KiB  
Article
Engineering of the CHAPk Staphylococcal Phage Endolysin to Enhance Antibacterial Activity against Stationary-Phase Cells
by Sara Arroyo-Moreno, Máire Begley, Kornelia Dembicka and Aidan Coffey
Antibiotics 2021, 10(6), 722; https://doi.org/10.3390/antibiotics10060722 - 16 Jun 2021
Cited by 6 | Viewed by 2987
Abstract
Bacteriophage endolysins and their derivatives have strong potential as antibacterial agents considering the increasing prevalence of antibiotic resistance in common bacterial pathogens. The peptidoglycan degrading peptidase CHAPk, a truncated derivate of staphylococcal phage K endolysin (LysK), has proven efficacy in preventing and disrupting [...] Read more.
Bacteriophage endolysins and their derivatives have strong potential as antibacterial agents considering the increasing prevalence of antibiotic resistance in common bacterial pathogens. The peptidoglycan degrading peptidase CHAPk, a truncated derivate of staphylococcal phage K endolysin (LysK), has proven efficacy in preventing and disrupting staphylococcal biofilms. Nevertheless, the concentration of CHAPk required to eliminate populations of stationary-phase cells was previously found to be four-fold higher than that for log-phase cells. Moreover, CHAPk-mediated lysis of stationary-phase cells was observed to be slower than for log-phase cultures. In the present study, we report the fusion of a 165 amino acid fragment containing CHAPk with a 136 amino acid fragment containing the cell-binding domain of the bacteriocin lysostaphin to create a chimeric enzyme designated CHAPk-SH3blys in the vector pET28a. The chimeric protein was employed in concentrations as low as 5 μg/mL, producing a reduction in turbidity in 7-day-old cultures, whereas the original CHAPk required at least 20 μg/mL to achieve this. Where 7-day old liquid cultures were used, the chimeric enzyme exhibited a 16-fold lower MIC than CHAPk. In terms of biofilm prevention, a concentration of 1 μg/mL of the chimeric enzyme was sufficient, whereas for CHAPk, 125 μg/mL was needed. Moreover, the chimeric enzyme exhibited total biofilm disruption when 5 μg/mL was employed in 4-h assays, whereas CHAPk could only partially disrupt the biofilms at this concentration. This study demonstrates that the cell-binding domain from lysostaphin can make the phage endolysin CHAPk more effective against sessile staphylococcal cells. Full article
(This article belongs to the Special Issue Development of Bacteriophage Derived Lysins and Depolymerases for Therapeutic Purposes in Combating Bacterial Pathogens)
►▼ Show Figures

Figure 1

12 pages, 1170 KiB  
Article
Rapid and High-Throughput Evaluation of Diverse Configurations of Engineered Lysins Using the VersaTile Technique
by Lisa Duyvejonck, Hans Gerstmans, Michiel Stock, Dennis Grimon, Rob Lavigne and Yves Briers
Antibiotics 2021, 10(3), 293; https://doi.org/10.3390/antibiotics10030293 - 11 Mar 2021
Cited by 9 | Viewed by 3068
Abstract
Bacteriophage-encoded lysins are an emerging class of antibacterial enzymes based on peptidoglycan degradation. The modular composition of lysins is a hallmark feature enabling optimization of antibacterial and pharmacological properties by engineering of lysin candidates based on lysin and non-lysin modules. In this regard, [...] Read more.
Bacteriophage-encoded lysins are an emerging class of antibacterial enzymes based on peptidoglycan degradation. The modular composition of lysins is a hallmark feature enabling optimization of antibacterial and pharmacological properties by engineering of lysin candidates based on lysin and non-lysin modules. In this regard, the recent introduction of the VersaTile technique allows the rapid construction of large modular lysin libraries based on a premade repository of building blocks. In this study, we perform a high-throughput construction and screening of five combinatorial lysin libraries with different configurations, targeting Klebsiella pneumoniae. An elaborate analysis of the activity distribution of 940 variants and sequencing data of 74 top hits inhibiting the growth of Klebsiella pneumoniae could be associated with specific design rules. Specific outer membrane permeabilizing peptides (OMPs) and enzymatically active domains (EADs) are significantly overrepresented among the top hits, while cell wall binding domains (CBDs) are equally represented. Especially libraries with the configuration (OMP–linker–CBD–EAD) and the inverse configuration (CBD–EAD–linker–OMP) yield the most active variants, with discernible clusters of variants that emerge above the remaining variants. The approach implemented here provides a blueprint for discovery campaigns of engineered lysins starting from libraries with different configurations and compositions. Full article
(This article belongs to the Special Issue Development of Bacteriophage Derived Lysins and Depolymerases for Therapeutic Purposes in Combating Bacterial Pathogens)
►▼ Show Figures

Figure 1

15 pages, 3660 KiB  
Article
Phage φAB6-Borne Depolymerase Combats Acinetobacter baumannii Biofilm Formation and Infection
by Md. Shahed-Al-Mahmud, Rakesh Roy, Febri Gunawan Sugiokto, Md. Nazmul Islam, Ming-Der Lin, Ling-Chun Lin and Nien-Tsung Lin
Antibiotics 2021, 10(3), 279; https://doi.org/10.3390/antibiotics10030279 - 09 Mar 2021
Cited by 40 | Viewed by 4830
Abstract
Biofilm formation is one of the main causes of increased antibiotic resistance in Acinetobacter baumannii infections. Bacteriophages and their derivatives, such as tail proteins with depolymerase activity, have shown considerable potential as antibacterial or antivirulence agents against bacterial infections. Here, we gained insights [...] Read more.
Biofilm formation is one of the main causes of increased antibiotic resistance in Acinetobacter baumannii infections. Bacteriophages and their derivatives, such as tail proteins with depolymerase activity, have shown considerable potential as antibacterial or antivirulence agents against bacterial infections. Here, we gained insights into the activity of a capsular polysaccharide (CPS) depolymerase, derived from the tailspike protein (TSP) of φAB6 phage, to degrade A. baumannii biofilm in vitro. Recombinant TSP showed enzymatic activity and was able to significantly inhibit biofilm formation and degrade formed biofilms; as low as 0.78 ng, the inhibition zone can still be formed on the bacterial lawn. Additionally, TSP inhibited the colonization of A. baumannii on the surface of Foley catheter sections, indicating that it can be used to prevent the adhesion of A. baumannii to medical device surfaces. Transmission and scanning electron microscopy demonstrated membrane leakage of bacterial cells treated with TSP, resulting in cell death. The therapeutic effect of TSP in zebrafish was also evaluated and the results showed that the survival rate was significantly improved (80%) compared with that of the untreated control group (10%). Altogether, we show that TSP derived from φAB6 is expected to become a new antibiotic against multi-drug resistant A. baumannii and a biocontrol agent that prevents the formation of biofilms on medical devices. Full article
(This article belongs to the Special Issue Development of Bacteriophage Derived Lysins and Depolymerases for Therapeutic Purposes in Combating Bacterial Pathogens)
►▼ Show Figures

Figure 1

14 pages, 713 KiB  
Article
A Putative Amidase Endolysin Encoded by Clostridium perfringens St13 Exhibits Specific Lytic Activity and Synergizes with the Muramidase Endolysin Psm
by Hiroshi Sekiya, Maho Okada, Eiji Tamai, Toshi Shimamoto, Tadashi Shimamoto and Hirofumi Nariya
Antibiotics 2021, 10(3), 245; https://doi.org/10.3390/antibiotics10030245 - 01 Mar 2021
Cited by 13 | Viewed by 2498
Abstract
Clostridium perfringens is an often-harmful intestinal bacterium that causes various diseases ranging from food poisoning to life-threatening fulminant disease. Potential treatments include phage-derived endolysins, a promising family of alternative antimicrobial agents. We surveyed the genome of the C. perfringens st13 strain and identified [...] Read more.
Clostridium perfringens is an often-harmful intestinal bacterium that causes various diseases ranging from food poisoning to life-threatening fulminant disease. Potential treatments include phage-derived endolysins, a promising family of alternative antimicrobial agents. We surveyed the genome of the C. perfringens st13 strain and identified an endolysin gene, psa, in the phage remnant region. Psa has an N-terminal catalytic domain that is homologous to the amidase_2 domain, and a C-terminal domain of unknown function. psa and gene derivatives encoding various Psa subdomains were cloned and expressed in Escherichia coli as N-terminal histidine-tagged proteins. Purified His-tagged full-length Psa protein (Psa-his) showed C. perfringens-specific lytic activity in turbidity reduction assays. In addition, we demonstrated that the uncharacterized C-terminal domain has cell wall-binding activity. Furthermore, cell wall-binding measurements showed that Psa binding was highly specific to C. perfringens. These results indicated that Psa is an amidase endolysin that specifically lyses C. perfringens; the enzyme’s specificity is highly dependent on the binding of the C-terminal domain. Moreover, Psa was shown to have a synergistic effect with another C. perfringens-specific endolysin, Psm, which is a muramidase that cleaves peptidoglycan at a site distinct from that targeted by Psa. The combination of Psa and Psm may be effective in the treatment and prevention of C. perfringens infections. Full article
(This article belongs to the Special Issue Development of Bacteriophage Derived Lysins and Depolymerases for Therapeutic Purposes in Combating Bacterial Pathogens)
►▼ Show Figures

Figure 1

11 pages, 1719 KiB  
Article
Simultaneous Control of Staphylococcus aureus and Bacillus cereus Using a Hybrid Endolysin LysB4EAD-LysSA11
by Bokyung Son, Minsuk Kong, Yoyeon Cha, Jaewoo Bai and Sangryeol Ryu
Antibiotics 2020, 9(12), 906; https://doi.org/10.3390/antibiotics9120906 - 14 Dec 2020
Cited by 15 | Viewed by 3221
Abstract
Bacteriophage endolysins have attracted attention as promising alternatives to antibiotics, and their modular structure facilitates endolysin engineering to develop novel endolysins with enhanced versatility. Here, we constructed hybrid proteins consisting of two different endolysins for simultaneous control of two critical foodborne pathogens, Staphylococcus [...] Read more.
Bacteriophage endolysins have attracted attention as promising alternatives to antibiotics, and their modular structure facilitates endolysin engineering to develop novel endolysins with enhanced versatility. Here, we constructed hybrid proteins consisting of two different endolysins for simultaneous control of two critical foodborne pathogens, Staphylococcus aureus and Bacillus cereus. The full-length or enzymatically active domain (EAD) of LysB4, an endolysin from the B. cereus-infecting phage B4, was fused to LysSA11, an endolysin of the S. aureus-infecting phage SA11, via a helical linker in both orientations. The hybrid proteins maintained the lytic activity of their parental endolysins against both S. aureus and B. cereus, but they showed an extended antimicrobial spectrum. Among them, the EAD of LysB4 fused with LysSA11 (LysB4EAD-LyaSA11) showed significantly increased thermal stability compared to its parental endolysins. LysB4EAD-LysSA11 exhibited high lytic activity at pH 8.0–9.0 against S. aureus and at pH 5.0–10.0 against B. cereus, but the lytic activity of the protein decreased in the presence of NaCl. In boiled rice, treatment with 3.0 µM of LysB4EAD-LysSA11 reduced the number of S. aureus and B. cereus to undetectable levels within 2 h and also showed superior antimicrobial activity to LyB4EAD and LysSA11 in combination. These results suggest that LysB4EAD-LysSA11 could be a potent antimicrobial agent for simultaneous control of S. aureus and B. cereus. Full article
(This article belongs to the Special Issue Development of Bacteriophage Derived Lysins and Depolymerases for Therapeutic Purposes in Combating Bacterial Pathogens)
►▼ Show Figures

Graphical abstract

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