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Szadkowska M, Kocot AM, Sowik D, Wyrzykowski D, Jankowska E, Kozlowski LP, Makowska J, Plotka M. Molecular characterization of the PhiKo endolysin from Thermus thermophilus HB27 bacteriophage phiKo and its cryptic lytic peptide RAP-29. Front Microbiol 2024; 14:1303794. [PMID: 38312500 PMCID: PMC10836841 DOI: 10.3389/fmicb.2023.1303794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/12/2023] [Indexed: 02/06/2024] Open
Abstract
Introduction In the era of increasing bacterial resistance to antibiotics, new bactericidal substances are sought, and lysins derived from extremophilic organisms have the undoubted advantage of being stable under harsh environmental conditions. The PhiKo endolysin is derived from the phiKo bacteriophage infecting Gram-negative extremophilic bacterium Thermus thermophilus HB27. This enzyme shows similarity to two previously investigated thermostable type-2 amidases, the Ts2631 and Ph2119 from Thermus scotoductus bacteriophages, that revealed high lytic activity not only against thermophiles but also against Gram-negative mesophilic bacteria. Therefore, antibacterial potential of the PhiKo endolysin was investigated in the study presented here. Methods Enzyme activity was assessed using turbidity reduction assays (TRAs) and antibacterial tests. Differential scanning calorimetry was applied to evaluate protein stability. The Collection of Anti-Microbial Peptides (CAMP) and Antimicrobial Peptide Calculator and Predictor (APD3) were used to predict regions with antimicrobial potential in the PhiKo primary sequence. The minimum inhibitory concentration (MIC) of the RAP-29 synthetic peptide was determined against Gram-positive and Gram-negative selected strains, and mechanism of action was investigated with use of membrane potential sensitive fluorescent dye 3,3'-Dipropylthiacarbocyanine iodide (DiSC3(5)). Results and discussion The PhiKo endolysin is highly thermostable with melting temperature of 91.70°C. However, despite its lytic effect against such extremophiles as: T. thermophilus, Thermus flavus, Thermus parvatiensis, Thermus scotoductus, and Deinococcus radiodurans, PhiKo showed moderate antibacterial activity against mesophiles. Consequently, its protein sequence was searched for regions with potential antibacterial activity. A highly positively charged region was identified and synthetized (PhiKo105-133). The novel RAP-29 peptide lysed mesophilic strains of staphylococci and Gram-negative bacteria, reducing the number of cells by 3.7-7.1 log units and reaching the minimum inhibitory concentration values in the range of 2-31 μM. This peptide is unstructured in an aqueous solution but forms an α-helix in the presence of detergents. Moreover, it binds lipoteichoic acid and lipopolysaccharide, and causes depolarization of bacterial membranes. The RAP-29 peptide is a promising candidate for combating bacterial pathogens. The existence of this cryptic peptide testifies to a much wider panel of antimicrobial peptides than thought previously.
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Affiliation(s)
- Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, University of Gdańsk, Gdańsk, Poland
| | - Aleksandra Maria Kocot
- Laboratory of Extremophiles Biology, Department of Microbiology, University of Gdańsk, Gdańsk, Poland
| | - Daria Sowik
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Dariusz Wyrzykowski
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Elzbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Lukasz Pawel Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warsaw, Poland
| | - Joanna Makowska
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdańsk, Gdańsk, Poland
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, University of Gdańsk, Gdańsk, Poland
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Carratalá JV, Arís A, Garcia-Fruitós E, Ferrer-Miralles N. Design strategies for positively charged endolysins: Insights into Artilysin development. Biotechnol Adv 2023; 69:108250. [PMID: 37678419 DOI: 10.1016/j.biotechadv.2023.108250] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 09/01/2023] [Accepted: 09/04/2023] [Indexed: 09/09/2023]
Abstract
Endolysins are bacteriophage-encoded enzymes that can specifically degrade the peptidoglycan layer of bacterial cell wall, making them an attractive tool for the development of novel antibacterial agents. The use of genetic engineering techniques for the production and modification of endolysins offers the opportunity to customize their properties and activity against specific bacterial targets, paving the way for the development of personalized therapies for bacterial infections. Gram-negative bacteria possess an outer membrane that can hinder the action of recombinantly produced endolysins. However, certain endolysins are capable of crossing the outer membrane by virtue of segments that share properties resembling those of cationic peptides. These regions increase the affinity of the endolysin towards the bacterial surface and assist in the permeabilization of the membrane. In order to improve the bactericidal effectiveness of endolysins, approaches have been implemented to increase their net charge, including the development of Artilysins containing positively charged amino acids at one end. At present, there are no specific guidelines outlining the steps for implementing these modifications. There is an ongoing debate surrounding the optimal location of positive charge, the need for a linker region, and the specific amino acid composition of peptides for modifying endolysins. The aim of this study is to provide clarity on these topics by analyzing and comparing the most effective modifications found in previous literature.
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Affiliation(s)
- Jose Vicente Carratalá
- Department of Ruminant Production, Institute of Agriculture and Agrifood Research and Technology (IRTA), Caldes de Montbui, 08140 Barcelona, Spain; Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, 08193 Barcelona, Spain; Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, 08193 Barcelona, Spain; Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain.
| | - Anna Arís
- Department of Ruminant Production, Institute of Agriculture and Agrifood Research and Technology (IRTA), Caldes de Montbui, 08140 Barcelona, Spain
| | - Elena Garcia-Fruitós
- Department of Ruminant Production, Institute of Agriculture and Agrifood Research and Technology (IRTA), Caldes de Montbui, 08140 Barcelona, Spain
| | - Neus Ferrer-Miralles
- Institute for Biotechnology and Biomedicine, Autonomous University of Barcelona, Bellaterra, 08193 Barcelona, Spain; Department of Genetics and Microbiology, Autonomous University of Barcelona, Bellaterra, 08193 Barcelona, Spain; Bioengineering, Biomaterials and Nanomedicine Networking Biomedical Research Centre (CIBER-BBN), C/Monforte de Lemos 3-5, 28029 Madrid, Spain
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3
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Sui B, Wang X, Zhao T, Zhen J, Ren H, Liu W, Zhang X, Zhang C. Design, Screening, and Characterization of Engineered Phage Endolysins with Extracellular Antibacterial Activity against Gram-Negative Bacteria. Appl Environ Microbiol 2023; 89:e0058123. [PMID: 37338346 PMCID: PMC10370328 DOI: 10.1128/aem.00581-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Accepted: 05/23/2023] [Indexed: 06/21/2023] Open
Abstract
Phage-encoded endolysins are emerging antibacterial agents based on their ability to efficiently degrade peptidoglycan on Gram-positive bacteria, but the envelope characteristics of Gram-negative bacteria limit their application. Engineering modifications of endolysins can improve the optimization of their penetrative and antibacterial properties. This study constructed a screening platform to screen for engineered Artificial-Bp7e (Art-Bp7e) endolysins with extracellular antibacterial activity against Escherichia coli. An oligonucleotide of 20 repeated NNK codons was inserted upstream of the endolysin gene Bp7e to construct a chimeric endolysin library in the pColdTF vector. The chimeric Art-Bp7e proteins were expressed by transforming the plasmid library into E. coli BL21 and released by chloroform fumigation, and the protein activities were evaluated by the spotting method and the colony-counting method to screen for promising proteins. Sequence analysis showed that all screened proteins with extracellular activities had a chimeric peptide with a positive charge and an α-helical structure. Also, a representative protein, Art-Bp7e6, was further characterized. It exhibited broad antibacterial activity against E. coli (7/21), Salmonella enterica serovar Enteritidis (4/10), Pseudomonas aeruginosa (3/10), and even Staphylococcus aureus (1/10). In the transmembrane process, the chimeric peptide of Art-Bp7e6 depolarized the host cell envelope, increased the permeability of the cell, and facilitated the movement of Art-Bp7e6 across the envelope to hydrolyze the peptidoglycan. In conclusion, the screening platform successfully screened for chimeric endolysins with extracellular antibacterial activities against Gram-negative bacteria, which provides methodological support for the further screening of engineered endolysins with high extracellular activities against Gram-negative bacteria. Also, the established platform showed broad application prospects and can be used to screen various proteins. IMPORTANCE The presence of the envelope in Gram-negative bacteria limits the use of phage endolysins, and engineering endolysins is an efficient way to optimize their penetrative and antibacterial properties. We built a platform for endolysin engineering and screening. A random peptide was fused with the phage endolysin Bp7e to construct a chimeric endolysin library, and engineered Artificial-Bp7e (Art-Bp7e) endolysins with extracellular activity against Gram-negative bacteria were successfully screened from the library. The purposeful Art-Bp7e had a chimeric peptide with an abundant positive charge and an α-helical structure, which led Bp7e to acquire the ability for the extracellular lysis of Gram-negative bacteria and showed a broad lysis spectrum. The platform provides a huge library capacity without the limitations of reported proteins or peptides. It can be utilized for the further screening of optimal endolysins against Gram-negative bacteria as well as for the screening of additional proteins with specific modifications.
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Affiliation(s)
- Bingrui Sui
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- School of Bioengineering, Dalian University of Technology, Dalian, China
| | - Xinrui Wang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Tianyi Zhao
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Jianyu Zhen
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Huiying Ren
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Wenhua Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Xiaoxuan Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Can Zhang
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
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4
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Galzitskaya OV. Creation of New Antimicrobial Peptides. Int J Mol Sci 2023; 24:ijms24119451. [PMID: 37298402 DOI: 10.3390/ijms24119451] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023] Open
Abstract
Antimicrobial peptides (AMPs) are natural compounds that exhibit potent antimicrobial activity against various microorganisms, including bacteria, fungi, and viruses [...].
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Affiliation(s)
- Oxana V Galzitskaya
- Institute of Protein Research, Russian Academy of Sciences, 142290 Pushchino, Russia
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, 142290 Pushchino, Russia
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5
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Deng H, Li M, Zhang Q, Gao C, Song Z, Chen C, Wang Z, Feng X. The Broad-Spectrum Endolysin LySP2 Improves Chick Survival after Salmonella Pullorum Infection. Viruses 2023; 15:v15040836. [PMID: 37112818 PMCID: PMC10142873 DOI: 10.3390/v15040836] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 03/19/2023] [Accepted: 03/22/2023] [Indexed: 03/29/2023] Open
Abstract
Salmonella pullorum causes typical “Bacillary White Diarrhea” and loss of appetite in chicks, which leads to the death of chicks in severe cases; thus, it is still a critical issue in China. Antibiotics are conventional medicines used for Salmonella infections; however, due to the extensive long-term use and even abuse of antibiotics, drug resistance becomes increasingly severe, making treating pullorum disease more difficult. Most of the endolysins are hydrolytic enzymes produced by bacteriophages to cleave the host’s cell wall during the final stage of the lytic cycle. A virulent bacteriophage, YSP2, of Salmonella was isolated in a previous study. A Pichia pastoris expression strain that can express the Salmonella bacteriophage endolysin was constructed efficiently, and the Gram-negative bacteriophage endolysin, LySP2, was obtained in this study. Compared with the parental phage YSP2, which can only lyse Salmonella, LySP2 can lyse Salmonella and Escherichia. The survival rate of Salmonella-infected chicks treated with LySP2 can reach up to 70% and reduce Salmonella abundance in the liver and intestine. The treatment group showed that LySP2 significantly improved the health of infected chicks and alleviated organ damage caused by Salmonella infection. In this study, the Salmonella bacteriophage endolysin was expressed efficiently by Pichia pastoris, and the endolysin LySP2 showed good potential for the treatment of pullorum disease caused by Salmonella pullorum.
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Affiliation(s)
- Hewen Deng
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Mengjiao Li
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Qiuyang Zhang
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Chencheng Gao
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Zhanyun Song
- Changchun Customs District, Changchun 130000, China
| | - Chunhua Chen
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Zhuo Wang
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
| | - Xin Feng
- College of Veterinary Medicine, Jilin University, Xi’an Street 5333#, Changchun 130062, China
- Correspondence: ; Tel.: +86-135-0430-0193
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6
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Pollenz RS, Bland J, Pope WH. Bioinformatic characterization of endolysins and holin-like membrane proteins in the lysis cassette of phages that infect Gordonia rubripertincta. PLoS One 2022; 17:e0276603. [PMID: 36395171 PMCID: PMC9671378 DOI: 10.1371/journal.pone.0276603] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Accepted: 10/11/2022] [Indexed: 11/19/2022] Open
Abstract
Holins are bacteriophage-encoded transmembrane proteins that function to control the timing of bacterial lysis event, assist with the destabilization of the membrane proton motive force and in some models, generate large "pores" in the cell membrane to allow the exit of the phage-encoded endolysin so they can access the peptidoglycan components of the cell wall. The lysis mechanism has been rigorously evaluated through biochemical and genetic studies in very few phages, and the results indicate that phages utilize endolysins, holins and accessory proteins to the outer membrane to achieve cell lysis through several distinct operational models. This observation suggests the possibility that phages may evolve novel variations of how the lysis proteins functionally interact in an effort to improve fitness or evade host defenses. To begin to address this hypothesis, the current study utilized a comprehensive bioinformatic approach to systematically identify the proteins encoded by the genes within the lysis cassettes in 16 genetically diverse phages that infect the Gram-positive Gordonia rubripertincta NRLL B-16540 strain. The results show that there is a high level of diversity of the various lysis genes and 16 different genome organizations of the putative lysis cassette, many which have never been described. Thirty-four different genes encoding holin-like proteins were identified as well as a potential holin-major capsid fusion protein. The holin-like proteins contained between 1-4 transmembrane helices, were not shared to a high degree amongst the different phages and are present in the lysis cassette in a wide range of combinations of up to 4 genes in which none are duplicated. Detailed evaluation of the transmembrane domains and predicted membrane topologies of the holin-like proteins show that many have novel structures that have not been previously characterized. These results provide compelling support that there are novel operational lysis models yet to be discovered.
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Affiliation(s)
- Richard S. Pollenz
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Jackson Bland
- Department of Cell Biology, Microbiology and Molecular Biology, University of South Florida, Tampa, Florida, United States of America
| | - Welkin H. Pope
- Science Department, Chatham University, Pittsburgh, Pennsylvania, United States of America
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7
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Szadkowska M, Olewniczak M, Kloska A, Jankowska E, Kapusta M, Rybak B, Wyrzykowski D, Zmudzinska W, Gieldon A, Kocot A, Kaczorowska AK, Nierzwicki L, Makowska J, Kaczorowski T, Plotka M. A Novel Cryptic Clostridial Peptide That Kills Bacteria by a Cell Membrane Permeabilization Mechanism. Microbiol Spectr 2022; 10:e0165722. [PMID: 36094301 PMCID: PMC9602519 DOI: 10.1128/spectrum.01657-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 08/23/2022] [Indexed: 12/31/2022] Open
Abstract
This work reports detailed characteristics of the antimicrobial peptide Intestinalin (P30), which is derived from the LysC enzyme of Clostridium intestinale strain URNW. The peptide shows a broader antibacterial spectrum than the parental enzyme, showing potent antimicrobial activity against clinical strains of Gram-positive staphylococci and Gram-negative pathogens and causing between 3.04 ± 0.12 log kill for Pseudomonas aeruginosa PAO1 and 7.10 ± 0.05 log kill for multidrug-resistant Acinetobacter baumannii KPD 581 at a 5 μM concentration. Moreover, Intestinalin (P30) prevents biofilm formation and destroys 24-h and 72-h biofilms formed by Acinetobacter baumannii CRAB KPD 205 (reduction levels of 4.28 and 2.62 log CFU/mL, respectively). The activity of Intestinalin is combined with both no cytotoxicity and little hemolytic effect against mammalian cells. The nuclear magnetic resonance and molecular dynamics (MD) data show a high tendency of Intestinalin to interact with the bacterial phospholipid cell membrane. Although positively charged, Intestinalin resides in the membrane and aggregates into small oligomers. Negatively charged phospholipids stabilize peptide oligomers to form water- and ion-permeable pores, disrupting the integrity of bacterial cell membranes. Experimental data showed that Intestinalin interacts with negatively charged lipoteichoic acid (logK based on isothermal titration calorimetry, 7.45 ± 0.44), causes membrane depolarization, and affects membrane integrity by forming large pores, all of which result in loss of bacterial viability. IMPORTANCE Antibiotic resistance is rising rapidly among pathogenic bacteria, becoming a global public health problem that threatens the effectiveness of therapies for many infectious diseases. In this respect, antimicrobial peptides appear to be an interesting alternative to combat bacterial pathogens. Here, we report the characteristics of an antimicrobial peptide (of 30 amino acids) derived from the clostridial LysC enzyme. The peptide showed killing activity against clinical strains of Gram-positive and Gram-negative pathogens. Experimental data and computational modeling showed that this peptide forms transmembrane pores, directly engaging the negatively charged phospholipids of the bacterial cell membrane. Consequently, dissipation of the electrochemical gradient across cell membranes affects many vital processes, such as ATP synthesis, motility, and transport of nutrients. This kind of dysfunction leads to the loss of bacterial viability. Our firm conviction is that the presented study will be a helpful resource in searching for novel antimicrobial peptides that could have the potential to replace conventional antibiotics.
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Affiliation(s)
- Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Michal Olewniczak
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Anna Kloska
- Department of Medical Biology and Genetics, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Elzbieta Jankowska
- Department of Biomedical Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Malgorzata Kapusta
- Department of Plant Cytology and Embryology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Bartosz Rybak
- Department of Environmental Toxicology, Faculty of Health Sciences with Institute of Maritime and Tropical Medicine, Medical University of Gdansk, Gdansk, Poland
| | - Dariusz Wyrzykowski
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Wioletta Zmudzinska
- Laboratory of Biopolymer Structure, Intercollegiate Faculty of Biotechnology, University of Gdansk and Medical University of Gdansk, Gdansk, Poland
| | - Artur Gieldon
- Laboratory of Simulation of Polymers, Department of Theoretical Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Aleksandra Kocot
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Lukasz Nierzwicki
- Department of Physical Chemistry, Gdansk University of Technology, Gdansk, Poland
| | - Joanna Makowska
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdansk, Gdansk, Poland
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Gdansk, Poland
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A Single Catalytic Endolysin Domain Plychap001: Characterization and Application to Control Vibrio Parahaemolyticus and Its Biofilm Directly. Foods 2022; 11:foods11111578. [PMID: 35681328 PMCID: PMC9180635 DOI: 10.3390/foods11111578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 05/14/2022] [Accepted: 05/24/2022] [Indexed: 11/17/2022] Open
Abstract
Endolysins are enzymes used by bacteriophages to cleave the host cell wall in the final stages of the lytic cycle. As such, they are considered promising antibacterial agents for controlling and combating multidrug-resistant (MDR) bacteria. However, the application of endolysins targeting Gram-negative bacteria is greatly hindered by the outer membrane on these bacteria. Lysqdvp001, an endolysin with modular structure, has been reported as one of the most efficient endolysins against the Gram-negative bacterium Vibrio parahaemolyticus. In this study, Plychap001, the truncated recombinant catalytic domain of Lysqdvp001, was demonstrated to exhibit a direct and efficient bactericidal activity against broad spectrum of V. parahaemolyticus strains. Plychap001 was shown to be highly stable and retain high bactericidal activity at high temperatures, over a wide pH range, and at high NaCl concentrations. Plychap001 also exhibited a synergistic lytic effect with EDTA. Additionally, Plychap001 was found to efficiently degrade and eliminate V. parahaemolyticus biofilms on polystyrene surfaces. Our study establishes Plychap001 as a promising method for controlling V. parahaemolyticus in the food industry.
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The Antibacterial Effect of PEGylated Carbosilane Dendrimers on P. aeruginosa Alone and in Combination with Phage-Derived Endolysin. Int J Mol Sci 2022; 23:ijms23031873. [PMID: 35163794 PMCID: PMC8836974 DOI: 10.3390/ijms23031873] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 01/27/2022] [Accepted: 02/02/2022] [Indexed: 12/12/2022] Open
Abstract
The search for new microbicide compounds is of an urgent need, especially against difficult-to-eradicate biofilm-forming bacteria. One attractive option is the application of cationic multivalent dendrimers as antibacterials and also as carriers of active molecules. These compounds require an adequate hydrophilic/hydrophobic structural balance to maximize the effect. Herein, we evaluated the antimicrobial activity of cationic carbosilane (CBS) dendrimers unmodified or modified with polyethylene glycol (PEG) units, against planktonic and biofilm-forming P. aeruginosa culture. Our study revealed that the presence of PEG destabilized the hydrophilic/hydrophobic balance but reduced the antibacterial activity measured by microbiological cultivation methods, laser interferometry and fluorescence microscopy. On the other hand, the activity can be improved by the combination of the CBS dendrimers with endolysin, a bacteriophage-encoded peptidoglycan hydrolase. This enzyme applied in the absence of the cationic CBS dendrimers is ineffective against Gram-negative bacteria because of the protective outer membrane shield. However, the endolysin-CBS dendrimer mixture enables the penetration through the membrane and then deterioration of the peptidoglycan layer, providing a synergic antimicrobial effect.
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Gp29 LysA of mycobacteriophage TM4 can hydrolyze peptidoglycan through an N-acetyl-muramoyl-L-alanine amidase activity. BIOCHIMICA ET BIOPHYSICA ACTA. PROTEINS AND PROTEOMICS 2022; 1870:140745. [PMID: 34906734 DOI: 10.1016/j.bbapap.2021.140745] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 12/06/2021] [Accepted: 12/07/2021] [Indexed: 01/09/2023]
Abstract
Bacteriophage endolysins are crucial for progeny release at the end of the lytic cycle. Mycobacteriophage's genomes carry a lysin A essential gene, whose product cleaves the peptidoglycan (PG) layer and a lysin B, coding for an esterase, that cleaves the linkage between the mycolic acids and the arabinogalactan-PG complex. Lysin A mycobacteriophage proteins are highly modular and in gp29 (LysA) of phage TM4 three distinctive domains were identified. By bioinformatics analysis the central module was previously found to be similar to an amidase-2 domain family with an N-acetylmuramoyl -L-alanine amidase activity. We demonstrated experimentally that purified LysA is able to lyse a suspension of Micrococcus lysodeikticus and can promote cell lysis when expressed in E. coli and Mycobacterium smegmatis. After incubation of LysA with MDP (Muramyl dipeptide, N-acetyl-muramyl-L-alanyl-D-isoglutamine) we detected the presence of N-acetylmuramic acid (NAcMur) and L-Ala- D- isoGlutamine (L-Ala-D-isoGln) corroborating the proposed muramidase activity of this enzyme. This protein was stabilized at acidic pH in the presence of Zn consistent with the increase of the enzymatic activity under these conditions. By homology modeling, we predicted that the Zn ion is coordinated by His 226, His 335, and Asp 347 and we also identified the amino acid Glu 290 as the catalytic residue. LysA activity was completely abolished in derived mutants on these key residues, suggesting that the PG hydrolysis solely relies on the central domain of the protein.
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11
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Sekiya H, Kamitori S, Nariya H, Matsunami R, Tamai E. Structural and biochemical characterization of the Clostridium perfringens-specific Zn 2+-dependent amidase endolysin, Psa, catalytic domain. Biochem Biophys Res Commun 2021; 576:66-72. [PMID: 34482025 DOI: 10.1016/j.bbrc.2021.08.085] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 08/27/2021] [Indexed: 11/19/2022]
Abstract
Phage-derived endolysins, enzymes that degrade peptidoglycans, have the potential to serve as alternative antimicrobial agents. Psa, which was identified as an endolysin encoded in the genome of Clostridium perfringens st13, was shown to specifically lyse C. perfringens. Psa has an N-terminal catalytic domain that is homologous to the Amidase_2 domain (PF01510), and a novel C-terminal cell wall-binding domain. Here, we determined the X-ray structure of the Psa catalytic domain (Psa-CD) at 1.65 Å resolution. Psa-CD has a typical Amidase_2 domain structure, consisting of a spherical structure with a central β-sheet surrounded by two α-helix groups. Furthermore, there is a Zn2+ at the center of Psa-CD catalytic reaction site, as well as a unique T-shaped substrate-binding groove consisting of two grooves on the molecule surface. We performed modeling study of the enzyme/substrate complex along with a mutational analysis, and demonstrated that the structure of the substrate-binding groove is closely related to the amidase activity. Furthermore, we proposed a Zn2+-mediated catalytic reaction mechanism for the Amidase_2 family, in which tyrosine constitutes part of the catalytic reaction site.
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Affiliation(s)
- Hiroshi Sekiya
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Shigehiro Kamitori
- Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan
| | - Hirofumi Nariya
- Laboratory of Food Microbiology, Graduate School of Human Life Sciences Food and Nutritional Sciences, Jumonji University, 2-1-28, Kansawa, Niiza, Saitama, 352-8510, Japan
| | - Risa Matsunami
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan
| | - Eiji Tamai
- Department of Infectious Disease, College of Pharmaceutical Sciences, Matsuyama University, 4-2 Bunkyo-cho, Matsuyama, Ehime, 790-8578, Japan; Life Science Research Center and Faculty of Medicine, Kagawa University, 1750-1, Ikenobe, Miki-cho, Kita-gun, Kagawa, 761-0793, Japan.
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12
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Morzywolek A, Plotka M, Kaczorowska AK, Szadkowska M, Kozlowski LP, Wyrzykowski D, Makowska J, Waters JJ, Swift SM, Donovan DM, Kaczorowski T. Novel Lytic Enzyme of Prophage Origin from Clostridium botulinum E3 Strain Alaska E43 with Bactericidal Activity against Clostridial Cells. Int J Mol Sci 2021; 22:ijms22179536. [PMID: 34502443 PMCID: PMC8430805 DOI: 10.3390/ijms22179536] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 01/13/2023] Open
Abstract
Clostridium botulinum is a Gram-positive, anaerobic, spore-forming bacterium capable of producing botulinum toxin and responsible for botulism of humans and animals. Phage-encoded enzymes called endolysins, which can lyse bacteria when exposed externally, have potential as agents to combat bacteria of the genus Clostridium. Bioinformatics analysis revealed in the genomes of several Clostridium species genes encoding putative N-acetylmuramoyl-l-alanine amidases with anti-clostridial potential. One such enzyme, designated as LysB (224-aa), from the prophage of C. botulinum E3 strain Alaska E43 was chosen for further analysis. The recombinant 27,726 Da protein was expressed and purified from E. coli Tuner(DE3) with a yield of 37.5 mg per 1 L of cell culture. Size-exclusion chromatography and analytical ultracentrifugation experiments showed that the protein is dimeric in solution. Bioinformatics analysis and results of site-directed mutagenesis studies imply that five residues, namely H25, Y54, H126, S132, and C134, form the catalytic center of the enzyme. Twelve other residues, namely M13, H43, N47, G48, W49, A50, L73, A75, H76, Q78, N81, and Y182, were predicted to be involved in anchoring the protein to the lipoteichoic acid, a significant component of the Gram-positive bacterial cell wall. The LysB enzyme demonstrated lytic activity against bacteria belonging to the genera Clostridium, Bacillus, Staphylococcus, and Deinococcus, but did not lyse Gram-negative bacteria. Optimal lytic activity of LysB occurred between pH 4.0 and 7.5 in the absence of NaCl. This work presents the first characterization of an endolysin derived from a C. botulinum Group II prophage, which can potentially be used to control this important pathogen.
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Affiliation(s)
- Agnieszka Morzywolek
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-822 Gdansk, Poland; (A.M.); (M.S.)
| | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-822 Gdansk, Poland; (A.M.); (M.S.)
- Correspondence: (M.P.); (T.K.)
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, 80-308 Gdansk, Poland;
| | - Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-822 Gdansk, Poland; (A.M.); (M.S.)
| | - Lukasz P. Kozlowski
- Institute of Informatics, Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, 02-097 Warsaw, Poland;
| | - Dariusz Wyrzykowski
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland; (D.W.); (J.M.)
| | - Joanna Makowska
- Department of General and Inorganic Chemistry, Faculty of Chemistry, University of Gdansk, 80-308 Gdansk, Poland; (D.W.); (J.M.)
| | - Jerel J. Waters
- Animal Biosciences and Biotechnology Laboratory, ARS, NEA, USDA, Beltsville, MD 20705-2350, USA; (J.J.W.); (S.M.S.); (D.M.D.)
| | - Steven M. Swift
- Animal Biosciences and Biotechnology Laboratory, ARS, NEA, USDA, Beltsville, MD 20705-2350, USA; (J.J.W.); (S.M.S.); (D.M.D.)
| | - David M. Donovan
- Animal Biosciences and Biotechnology Laboratory, ARS, NEA, USDA, Beltsville, MD 20705-2350, USA; (J.J.W.); (S.M.S.); (D.M.D.)
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, 80-822 Gdansk, Poland; (A.M.); (M.S.)
- Correspondence: (M.P.); (T.K.)
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13
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Aevarsson A, Kaczorowska AK, Adalsteinsson BT, Ahlqvist J, Al-Karadaghi S, Altenbuchner J, Arsin H, Átlasson ÚÁ, Brandt D, Cichowicz-Cieślak M, Cornish KAS, Courtin J, Dabrowski S, Dahle H, Djeffane S, Dorawa S, Dusaucy J, Enault F, Fedøy AE, Freitag-Pohl S, Fridjonsson OH, Galiez C, Glomsaker E, Guérin M, Gundesø SE, Gudmundsdóttir EE, Gudmundsson H, Håkansson M, Henke C, Helleux A, Henriksen JR, Hjörleifdóttir S, Hreggvidsson GO, Jasilionis A, Jochheim A, Jónsdóttir I, Jónsdóttir LB, Jurczak-Kurek A, Kaczorowski T, Kalinowski J, Kozlowski LP, Krupovic M, Kwiatkowska-Semrau K, Lanes O, Lange J, Lebrat J, Linares-Pastén J, Liu Y, Lorentsen SA, Lutterman T, Mas T, Merré W, Mirdita M, Morzywołek A, Ndela EO, Karlsson EN, Olgudóttir E, Pedersen C, Perler F, Pétursdóttir SK, Plotka M, Pohl E, Prangishvili D, Ray JL, Reynisson B, Róbertsdóttir T, Sandaa RA, Sczyrba A, Skírnisdóttir S, Söding J, Solstad T, Steen IH, Stefánsson SK, Steinegger M, Overå KS, Striberny B, Svensson A, Szadkowska M, Tarrant EJ, Terzian P, Tourigny M, Bergh TVD, Vanhalst J, Vincent J, Vroling B, Walse B, Wang L, Watzlawick H, Welin M, Werbowy O, Wons E, Zhang R. Going to extremes - a metagenomic journey into the dark matter of life. FEMS Microbiol Lett 2021; 368:6296640. [PMID: 34114607 DOI: 10.1093/femsle/fnab067] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Accepted: 06/08/2021] [Indexed: 02/06/2023] Open
Abstract
The Virus-X-Viral Metagenomics for Innovation Value-project was a scientific expedition to explore and exploit uncharted territory of genetic diversity in extreme natural environments such as geothermal hot springs and deep-sea ocean ecosystems. Specifically, the project was set to analyse and exploit viral metagenomes with the ultimate goal of developing new gene products with high innovation value for applications in biotechnology, pharmaceutical, medical, and the life science sectors. Viral gene pool analysis is also essential to obtain fundamental insight into ecosystem dynamics and to investigate how viruses influence the evolution of microbes and multicellular organisms. The Virus-X Consortium, established in 2016, included experts from eight European countries. The unique approach based on high throughput bioinformatics technologies combined with structural and functional studies resulted in the development of a biodiscovery pipeline of significant capacity and scale. The activities within the Virus-X consortium cover the entire range from bioprospecting and methods development in bioinformatics to protein production and characterisation, with the final goal of translating our results into new products for the bioeconomy. The significant impact the consortium made in all of these areas was possible due to the successful cooperation between expert teams that worked together to solve a complex scientific problem using state-of-the-art technologies as well as developing novel tools to explore the virosphere, widely considered as the last great frontier of life.
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Affiliation(s)
| | - Anna-Karina Kaczorowska
- Collection of Plasmids and Microorganisms, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Josefin Ahlqvist
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Joseph Altenbuchner
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hasan Arsin
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - David Brandt
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Magdalena Cichowicz-Cieślak
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Katy A S Cornish
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | | | - Håkon Dahle
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,Department of Informatics, University of Bergen, PO Box 7803, Thormøhlens gate 53 A/B, N-5020 Bergen, Norway
| | | | - Sebastian Dorawa
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | | | - Francois Enault
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Anita-Elin Fedøy
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Stefanie Freitag-Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | | | - Clovis Galiez
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Eirin Glomsaker
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | - Sigurd E Gundesø
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | | | | | - Maria Håkansson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Christian Henke
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | | | | | - Gudmundur O Hreggvidsson
- Matis ohf, Vinlandsleid 12, Reykjavik 113, Iceland.,Faculty of Life and Environmental Sciences, University of Iceland, Askja-Sturlugata 7, Reykjavik, Iceland
| | - Andrius Jasilionis
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Annika Jochheim
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | | | - Agata Jurczak-Kurek
- Department of Molecular Evolution, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Tadeusz Kaczorowski
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Jörn Kalinowski
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Lukasz P Kozlowski
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany.,Institute of Informatics, Faculty of Mathematics, Informatics, and Mechanics, University of Warsaw, Banacha 2, Warsaw 02-097, Poland
| | - Mart Krupovic
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Karolina Kwiatkowska-Semrau
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Olav Lanes
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Joanna Lange
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | | | - Javier Linares-Pastén
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | - Ying Liu
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | | | - Tobias Lutterman
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany
| | - Thibaud Mas
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | - Milot Mirdita
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Agnieszka Morzywołek
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Eric Olo Ndela
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Eva Nordberg Karlsson
- Biotechnology, Department of Chemistry, Lund University, PO Box 124, Naturvetarvägen 14/Sölvegatan 39 A, SE-221 00 Lund, Sweden
| | | | - Cathrine Pedersen
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Francine Perler
- Perls of Wisdom Biotech Consulting, 74 Fuller Street, Brookline, MA 02446, USA
| | | | - Magdalena Plotka
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ehmke Pohl
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom.,Department of Biosciences, Durham University, South Road, Durham DH1 3LE, UK
| | - David Prangishvili
- Institute Pasteur, Department of Microbiology, 25-28 Rue du Dr Roux, 75015 Paris, France
| | - Jessica L Ray
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway.,NORCE Environment, NORCE Norwegian Research Centre AS, Nygårdsgaten 112, 5008 Bergen, Norway
| | | | | | - Ruth-Anne Sandaa
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | - Alexander Sczyrba
- Center for Biotechnology, Bielefeld University, Universitätsstraße 27, Bielefeld 33615, Germany.,Computational Metagenomics, Bielefeld University, Universitätsstraße 27, 30501 Bielefeld, Germany
| | | | - Johannes Söding
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Terese Solstad
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Ida H Steen
- Department of Biological Sciences, University of Bergen, PO Box 7803, Thormøhlens gate 55, N-5020 Bergen, Norway
| | | | - Martin Steinegger
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | | | - Bernd Striberny
- ArcticZymes Technologies PO Box 6463, Sykehusveien 23, 9294 Tromsø, Norway
| | - Anders Svensson
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Monika Szadkowska
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Emma J Tarrant
- Department of Chemistry, Durham University, South Road, Durham DH1 3LE, United Kingdom
| | - Paul Terzian
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | | | | | | | - Jonathan Vincent
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, 49 Boulevard François-Mitterrand - CS 60032, UMR 6023, Clermont-Ferrand, France
| | - Bas Vroling
- Bio-Prodict, Nieuwe Marktstraat 54E 6511AA Nijmegen, Netherlands
| | - Björn Walse
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Lei Wang
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Hildegard Watzlawick
- Institute for Industrial Genetics, University of Stuttgart, Allmandring 31, 70569 Stuttgart, Germany
| | - Martin Welin
- SARomics Biostructures, Scheelevägen 2, SE-223 81 Lund, Sweden
| | - Olesia Werbowy
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ewa Wons
- Laboratory of Extremophiles Biology, Department of Microbiology, Faculty of Biology, University of Gdansk, Wita Stwosza 59, Gdansk 80-308, Poland
| | - Ruoshi Zhang
- Quantitative and Computational Biology, Max-Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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14
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Storey N, Rabiey M, Neuman BW, Jackson RW, Mulley G. Genomic Characterisation of Mushroom Pathogenic Pseudomonads and Their Interaction with Bacteriophages. Viruses 2020; 12:E1286. [PMID: 33182769 PMCID: PMC7696170 DOI: 10.3390/v12111286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 11/02/2020] [Accepted: 11/05/2020] [Indexed: 01/16/2023] Open
Abstract
Bacterial diseases of the edible white button mushroom Agaricus bisporus caused by Pseudomonas species cause a reduction in crop yield, resulting in considerable economic loss. We examined bacterial pathogens of mushrooms and bacteriophages that target them to understand the disease and opportunities for control. The Pseudomonastolaasii genome encoded a single type III protein secretion system (T3SS), but contained the largest number of non-ribosomal peptide synthase (NRPS) genes, multimodular enzymes that can play a role in pathogenicity, including a putative tolaasin-producing gene cluster, a toxin causing blotch disease symptom. However, Pseudomonasagarici encoded the lowest number of NRPS and three putative T3SS while non-pathogenic Pseudomonas sp. NS1 had intermediate numbers. Potential bacteriophage resistance mechanisms were identified in all three strains, but only P. agarici NCPPB 2472 was observed to have a single Type I-F CRISPR/Cas system predicted to be involved in phage resistance. Three novel bacteriophages, NV1, ϕNV3, and NV6, were isolated from environmental samples. Bacteriophage NV1 and ϕNV3 had a narrow host range for specific mushroom pathogens, whereas phage NV6 was able to infect both mushroom pathogens. ϕNV3 and NV6 genomes were almost identical and differentiated within their T7-like tail fiber protein, indicating this is likely the major host specificity determinant. Our findings provide the foundations for future comparative analyses to study mushroom disease and phage resistance.
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Affiliation(s)
- Nathaniel Storey
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
| | - Mojgan Rabiey
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Benjamin W. Neuman
- Biology Department, College of Arts, Sciences and Education, TAMUT, Texarkana, TX 75503, USA;
| | - Robert W. Jackson
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
- School of Biosciences and Birmingham Institute of Forest Research, University of Birmingham, Birmingham B15 2TT, UK
| | - Geraldine Mulley
- School of Biological Sciences, Whiteknights Campus, University of Reading, Reading RG6 6AJ, UK; (N.S.); (R.W.J.); (G.M.)
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15
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Wang F, Xiong Y, Xiao Y, Han J, Deng X, Lin L. MMPphg from the thermophilic Meiothermus bacteriophage MMP17 as a potential antimicrobial agent against both Gram-negative and Gram-positive bacteria. Virol J 2020; 17:130. [PMID: 32843096 PMCID: PMC7448439 DOI: 10.1186/s12985-020-01403-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 08/16/2020] [Indexed: 01/21/2023] Open
Abstract
Background New strategies are urgently needed to deal with the growing problem of multidrug-resistant bacterial pathogens. As the natural viruses against bacteria, recently, bacteriophages have received particular attention. Here, we identified and characterized a novel peptidoglycan hydrolase named MMPphg by decoding the complete genome sequence of Meiothermus bacteriophage MMP17, which was isolated in Tengchong hot spring in China and contains a circular genome of 33,172 bp in size and a GC content of 63.4%. Findings We cloned the MMPphg gene, overproduced and purified the phage lytic protein, which contains a highly conserved M23 metallopeptidase domain and can be activated by Mg2+ and Zn2+. MMPphg is capable of withstanding temperatures up to 70 °C, and preserved more than 80% of its activity after a 30 min treatment between 35 and 65 °C. More interestingly, by disrupting bacterial cells, MMPphg exhibits surprising antimicrobial activity against both Gram-negative and Gram-positive pathogenic bacteria, especially antibiotic-resistant strains such as Escherichia coli O157, Staphylococcus aureus and Klebsiella pneumonia. Conclusions In the current age of mounting antibiotic resistance, these results suggest the great potential of MMPphg, the gene product of bacteriophage MMP17, in combating bacterial infections and shed light on bacteriophage-based strategies to develop alternatives to conventional antibiotics for human or veterinary applications.
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Affiliation(s)
- Feng Wang
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan Province, China
| | - Yan Xiong
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan Province, China
| | - Yao Xiao
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan Province, China
| | - Jian Han
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan Province, China
| | - Xianyu Deng
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan Province, China
| | - Lianbing Lin
- Faculty of Life Science and Technology, Kunming University of Science and Technology, 727 South Jingming Road, Kunming, 650500, Yunnan Province, China. .,Engineering Research Center for Replacement Technology of Feed Antibiotics of Yunnan College, 727 South Jingming Road, Kunming, 650500, Yunnan Province, China.
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