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Engineering of Antibacterial Phage-Derived Proteins
Stockholm University, Faculty of Science, Department of Molecular Biosciences, The Wenner-Gren Institute.
2021 (English)Doctoral thesis, comprehensive summary (Other academic)
Abstract [en]

The increasing threat of antibiotic resistance calls for the development of new treatment methods. Bacteriophages are interesting candidates since they can lyse bacteria with great efficiency. Bacteriophages produce enzymes called endolysins which break down the peptidoglycan in the cell wall at the end of the infection cycle. The endolysins are also of great interest to use against bacteria since they can lyse cells from the outside, when the peptidoglycan is accessible.  When using bacteriophages and endolysins as therapeutics there is a risk that the human immune system will react to them since they are foreign particles. The lysate from the bacteria can cause the immune system to react with a massive release of cytokines. The plasma half-life can also become short since the protein is cleared from the blood stream. With protein engineering it is possible to combine functional domains from different proteins to construct new chimeric proteins, these domains can also be optimized for new functions through modification.  

In project 1 a chimeric protein was created that contained a cell wall binding domain from an endolysin and a domain from another protein that binds to IgG. Assays were made to see if the chimeric protein could attach non-specific IgG to bacteria and if this could induce binding of phagocytes to the bacteria. Induction of phagocytosis can potentially help clear the infection with lower risk of cytokine release, because the bacterial lysate will not be released. 

In project 2 the endolysin SAL-1 and the enzyme dispersin B were fused respectively with the spider silk protein 4RepCT to create antibacterial coatings. The ability of SAL-1-4RepCT to break down bacteria in the liquid surrounding the surface was measured. The dispersin B-4RepCt was examined for its ability to prevent biofilm formation.

Project 3 characterized the bacteriophage SU57. Both host interaction parameters and the genome were examined. One challenge that phage treatment faces is that bacteriophages can only be added in low concentrations and must thus multiply in situ. This requires that the bacteriophage has a large burst size while having a high adsorption rate and short latency period. To assess promising bacteriophages it is important to be able to decipher their genome. 

The goal of project 4 was to find the tertiary structure and active site of the endolysin SU57e. Bioinformatics were used to predict properties of the protein, the tertiary structure and the active site. Attempts were made to produce and purify the protein in order to enable crystallization for X-ray crystallography. 

Overall the projects in this thesis aim to increases the knowledge of the use of bacteriophages and phage derived proteins as antibacterials.

Place, publisher, year, edition, pages
Stockholm: Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University , 2021. , p. 45
Keywords [en]
Protein engineering, endolysin, IgG, linker protein, chimeric protein, artificial opsonin, spider silk, antibacterial surface, bacteriophage, structure prediction
National Category
Biological Sciences Microbiology
Research subject
Molecular Bioscience
Identifiers
URN: urn:nbn:se:su:diva-193720ISBN: 978-91-7911-520-3 (print)ISBN: 978-91-7911-521-0 (electronic)OAI: oai:DiVA.org:su-193720DiVA, id: diva2:1566412
Public defence
2021-09-06, Vivi Täckholmsalen (Q-salen), NPQ-huset, Svante Arrhenius väg 20, Stockholm, 10:00 (English)
Opponent
Supervisors
Available from: 2021-08-12 Created: 2021-06-15 Last updated: 2022-02-25Bibliographically approved
List of papers
1. Improved bacteria-phagocyte interaction by means of a fusion protein binding Staphylococcus peptidoglycan and Immunoglobulin G
Open this publication in new window or tab >>Improved bacteria-phagocyte interaction by means of a fusion protein binding Staphylococcus peptidoglycan and Immunoglobulin G
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(English)Manuscript (preprint) (Other academic)
Abstract [en]

The immune system plays an important role in the body´s defense against bacterial infections. Here, we hypothesize that adding an artificial opsonin that binds to antigens on the surface of infecting bacteria as well as to endogenous IgG can increase the interaction between bacteria and immune cells. A chimeric protein was made by fusion of the Src homology domain 3b (SH3b) from the Staphylococcus phage K endolysin (LysK) and the IgG-binding C2 domain from Streptococcus Protein G. SH3b binds to the bacterial cell wall of staphylococci and the C2 domain to the Fab region of the IgG which in turn binds to the Fc receptors of the phagocytes, facilitating interaction between phagocytes and bacteria. Comparative experiments with and without the chimeric protein showed that it both increased the amount of Staphylococcus carnosus cells bound by a humanized monoclonal IgG1 with unrelated specificity and increased the interaction of phagocytes with bacteria. The results justify development of chimeric proteins with the ability to act as artificial opsonins since these possibly can become an addition to future treatments of infections caused by antibiotic resistant bacteria.

Keywords
IgG Linker-protien SH3b C2
National Category
Natural Sciences
Research subject
Molecular Biology
Identifiers
urn:nbn:se:su:diva-193629 (URN)
Available from: 2021-06-03 Created: 2021-06-03 Last updated: 2022-02-25Bibliographically approved
2. Recombinant spider silk coatings functionalized with enzymes targeting bacteria and biofilms
Open this publication in new window or tab >>Recombinant spider silk coatings functionalized with enzymes targeting bacteria and biofilms
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2020 (English)In: MicrobiologyOpen, E-ISSN 2045-8827, Vol. 9, no 4, article id e993Article in journal (Refereed) Published
Abstract [en]

Bacteria forming biofilms on surgical implants is a problem that might be alleviated by the use of antibacterial coatings. In this article, recombinant spider silk was functionalized with the peptidoglycan degrading endolysin SAL-1 from the staphylococcal bacteriophage SAP-1 and the biofilm-matrix-degrading enzyme Dispersin B from Aggregatibacter actinomycetemcomitans using direct genetic fusion and/or covalent protein-protein fusion catalyzed by Sortase A. Spider silk assembly and enzyme immobilization was monitored using quartz crystal microbalance analysis. Enzyme activity was investigated both with a biochemical assay using cleavage of fluorescent substrate analogues and bacterial assays for biofilm degradation and turbidity reduction. Spider silk coatings functionalized with SAL-1 and Disperin B were found to exhibit bacteriolytic effect and inhibit biofilm formation, respectively. The strategy to immobilize antibacterial enzymes to spider silk presented herein show potential to be used as surface coatings of surgical implants and other medical equipment to avoid bacterial colonization.

Keywords
antibacterial, antibiofilm, coating, endolysin, recombinant spider silk
National Category
Biological Sciences Medical Materials
Identifiers
urn:nbn:se:su:diva-179505 (URN)10.1002/mbo3.993 (DOI)000511533600001 ()32032479 (PubMedID)
Available from: 2020-03-09 Created: 2020-03-09 Last updated: 2025-02-09Bibliographically approved
3. Infection Kinetics and Phylogenetic Analysis of vB_EcoD_SU57, a Virulent T1-Like Drexlerviridae Coliphage
Open this publication in new window or tab >>Infection Kinetics and Phylogenetic Analysis of vB_EcoD_SU57, a Virulent T1-Like Drexlerviridae Coliphage
2020 (English)In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 11, article id 565556Article in journal (Refereed) Published
Abstract [en]

The morphology, infection kinetics, genome sequence and phylogenetic characterization of the previously isolated bacteriophage vB_EcoD_SU57 are presented. The phage vB_EcoD_SU57 was isolated on Escherichia coli strain ECOR57 from the E. coli reference collection and was shown to produce four mm clear plaques with halos. Infection kinetics, as assessed by one-step growth analyses, suggest that vB_EcoD_SU57 is a virulent phage with an adsorption rate of 8.5 × 10–10 mL × min–1, a latency period of 14 min, and a burst size of 13 PFU per bacterium. Transmission electron microscopy confirmed vB_EcoD_SU57 to be a phage that used to be classified as a Siphoviridae phage. Bioinformatics analyses showed that the genome was 46,150 base pairs long, contained 29 genes with predicted protein functions, and 51 open reading frames encoding proteins with unknown function, many of which were gathered in clusters. A putative tRNA gene was also identified. Phylogenetic analyses showed that vB_EcoD_SU57 is a Braunvirinae phage of the newly formed Drexlerviridae family and closely related to T1-like E. coli phages vB_EcoS_ACG-M12 (Guelphvirus) and Rtp (Rtpvirus) as well as the unclassified phages vB_EcoS_CEB_EC3a and ECH1.

Keywords
T1-like bacteriophage, phage virulence, phage infection kinetics, phage phylogenetics, Drexlerviridae
National Category
Biological Sciences
Identifiers
urn:nbn:se:su:diva-188728 (URN)10.3389/fmicb.2020.565556 (DOI)000593921900001 ()33329423 (PubMedID)
Available from: 2021-01-19 Created: 2021-01-19 Last updated: 2024-01-17Bibliographically approved
4. Structure prediction of endolysin SU57e
Open this publication in new window or tab >>Structure prediction of endolysin SU57e
(English)Manuscript (preprint) (Other academic)
Abstract [en]

Endolysins are used by bacteriophages to break down the cell wall of the bacterial host towards the end of the infection cycle. Endolysins are interesting options for the creation of antibacterial substances and domains from endolysins can be combined with domains from other proteins to create antibacterial constructs. This article aims to find the tertiary structure and the enzymatically active site of the endolysin SU57e. This is done through the use of bioinformatics software, comparative analysis with other endolysins, and attempts at producing and purifying the protein for crystallization. SU57e is encoded by the phage vB_EcoD_SU57 (SU57) previously characterized by Koonjan et al. Bioinformatics analysis indicates that the structure is similar to that of endolysin R21 presented by Sun et al. SU57e also appears to have a signal-anchor-release-domain similar to that of R21. 

Keywords
SU57e structure
National Category
Natural Sciences
Research subject
Molecular Biology
Identifiers
urn:nbn:se:su:diva-193630 (URN)
Available from: 2021-06-03 Created: 2021-06-03 Last updated: 2022-02-25Bibliographically approved

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